https://wiki.flybase.org/mediawiki/api.php?action=feedcontributions&user=Sian&feedformat=atomFlyBase Wiki - User contributions [en]2024-03-28T09:36:53ZUser contributionsMediaWiki 1.35.3https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=170732FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2020-04-17T21:09:26Z<p>Sian: /* Posters */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* CanFly XV, June 2019. What's new in FlyBase? [[Media:CanFly2019.pdf|presentation]] (35 slides)<br />
* Boston Area Drosophila Meeting, June 2019. FlyBase Updates: Exploring the spectrum of Experimental Tools on FlyBase. [[Media:BADM_2019.pdf|presentation]] (11 slides)<br />
* ISB 2019. Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. [[Media:Biocurator2019_enzyme_talk.pdf|presentation]] (10 slides)<br />
* ADRC 2019. FlyBase updates 2019. [[Media:FlyBase updates 2019.pdf|presentation]] (18 slides)<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* TAGC 2020. What's new in FlyBase. [[Media:TAGC2020_whats_new.pdf|pdf]]<br />
* EDRC 2019. Systematising knowledge of Drosophila pathway members to fuel biological discovery. [[Media:EDRC2019-Pathways.pdf|pdf]]<br />
* EDRC 2019. What's New in FlyBase. [[Media:EDRC_2019_whats_new.pdf|pdf]]<br />
* ISB 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ISB2019-Pathways.pdf|pdf]]<br />
* ISB 2019. Experimental tools: a new way to categorise transgenic alleles in FlyBase. [[Media:ISB2019_experimental_tools.pdf|pdf]]<br />
* ISB 2019. The Drosophila Anatomy Ontology. [[Media:ISB2019_DAO.pdf|pdf]]<br />
* ADRC 2019. FlyBase: A Valuable Source of Molecular Interaction Data. [[Media:fb_poster.pdf|pdf]]<br />
* ADRC 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ADRC_2019_Pathways.pdf|pdf]]<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* EDRC 2017. Function-centered approaches for finding and analyzing genes within FlyBase. [[Media:EDRC_poster_function.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2019. New tools, features, and resources for 2019. [[Media:ADRC2019_NewTools.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:TAGC2020_whats_new.pdf&diff=170731File:TAGC2020 whats new.pdf2020-04-17T21:07:18Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Downloads_Overview&diff=170690FlyBase:Downloads Overview2020-02-11T21:50:18Z<p>Sian: /* Transposable elements (canonical set) (transposon_sequence_set.embl.txt) */</p>
<hr />
<div>==Introduction==<br />
<br />
The [http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page] is a web interface allowing easy access to the main directories and the individual bulk data files available at the [ftp://ftp.flybase.net/releases/current/ current FlyBase FTP repository]. Files can be downloaded either directly through the web interface or by connecting to the FTP site using an ftp client such as wget. '''Note that the Safari browser does not support browsing of FTP site directories, though it does allow download of individual files.''' The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
===Opening compressed files===<br />
Most of the files are compressed with the [http://www.gzip.org/ GNU gzip] program and have the suffix '.gz'. Most modern computers will unpack and open these files automatically after download. Alternatively, the gunzip command may be used on machines runnign Apple OS X or Unix. On a Windows machine we suggest you use the program [http://www.7-zip.org/ 7-zip] to open these files as several people have reported problems using WinZip. The resulting file should open with any standard text editor.<br />
<br />
===Archived Data===<br />
Data files from previous releases, as well as links to servers hosting older releases of FlyBase, can be accessed via the [http://{{flybaseorg}}/downloads/archivedata Archived Data] webpage.<br />
<br />
Using an FTP client, data files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve the 'fbgn_annotation_ID' file for the FB2018_06 release, type:<br />
<br />
<code><br />
wget <nowiki>"ftp://ftp.flybase.net/releases/FB2018_06/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz"</nowiki><br />
</code><br />
<br />
or more specifically:<br />
<br />
<code><br />
wget <nowiki>ftp://ftp.flybase.net/releases/FB2018_06/precomputed_files/genes/fbgn_annotation_ID_fb_2018_06.tsv.gz</nowiki><br />
</code><br />
<br />
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file.<br />
<br />
==Main Data Set==<br />
<br />
This section contains links to top-level directories of the [ftp://ftp.flybase.net/releases/current/ FlyBase FTP repository].<br />
<br />
===Postgres Chado Database Dump===<br />
<br />
The Chado database link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:<br />
$ psql -h chado.flybase.org -U flybase flybase<br />
<br />
The version running on this service is identical to the current web site release.<br />
<br />
===Drosophila Data===<br />
<br />
This section contains links to:<br />
* the [ftp://ftp.flybase.net/releases/current/ current FTP repository], containing all files for the current FlyBase release<br />
<br />
* the [ftp://ftp.flybase.net/releases/current/chado-xml current Chado-XML repository], containing the chado XML files generated from the PostgreSQL database for each FlyBase data class for the current FlyBase release. These files contain all the information used to generate FlyBase report pages and reflect the organization of the data in the database. The DTDs for these XML files, listing the structure of the files, are included in this directory.<br />
<br />
* the [ftp://ftp.flybase.net/genomes/ Genomes FTP repository], containing genome and genome annotation data files (including FASTA, GFF and GTF files) for D. melanogaster and other Drosophila species, organized by genome/FlyBase release number. For release FB2018_05 and earlier, data are available for each of the original 12 sequenced Drosophila species. From release FB2018_06 onward, data are available only for D. melanogaster, D. simulans, D. ananassae, D. pseudoobscura and D. virilis.<br />
<br />
==Bulk data files==<br />
<br />
The remaining sections of the [http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page] are organized by data class/type and provide direct downloads of the current bulk data files from the FTP site. Most files are from the [ftp://ftp.flybase.net/releases/current/precomputed_files/ current precomputed files] directory of the FTP site and contain useful data for the specified data type (described in detail below). The [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview#Genomes:_Annotation_and_Sequence Genomes] files are from the [ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current current D. melanogaster FTP genomes directory] or the current files for selected other Drosophila species.<br />
<br />
The first part of a filename always describes the content of the file, and the second part may contain a FlyBase or genome annotation version number. For example, the file "fbgn_annotation_ID_fb_2018_06.tsv.gz" maps the primary FlyBase gene identifiers (FBgn) to their annotation IDs for the FB2018_06 release of FlyBase. The "dmel-all-CDS-r6.25.fasta.gz" files contains the coding sequences for all D. melanogaster genes from the release 6 of the sequence assembly, annotation release 25.<br />
<br />
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.<br />
<br />
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.<br />
<br />
Each precomputed data file contains the complete data set for the FlyBase release. If you are looking for information on a defined subset of genes or other FlyBase data type, you can use the [http://{{flybaseorg}}/batchdownload Batch Download] tool to query the precomputed data files and thus obtain only the data you require. This approach is described in more detail [https://wiki.flybase.org/wiki/FlyBase:Batch_Download here].<br />
<br />
<br />
===Synonyms===<br />
<br />
====FlyBase Synonyms (fb_synonym_*.tsv)====<br />
The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).<br />
<br />
The file includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
* genes from drosophilid species and genes from non-drosophilids that have been introduced into transgenic flies<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''primary_FBid''' <br />
|Primary FlyBase identifier for the object.<br />
|-<br />
|'''organism_abbreviation''' <br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin.<br />
|-<br />
|'''current_symbol'''<br />
|Current symbol used in FlyBase for the object.<br />
|-<br />
|'''current_fullname''' <br />
|Current full name used in FlyBase for the object.<br />
|-<br />
|'''fullname_synonym(s)''' <br />
|Non-current full name(s) associated with the object (comma separated values).<br />
|-<br />
|'''symbol_synonym(s)'''<br />
|Non-current symbol(s) associated with the object (comma separated values).<br />
|-<br />
|}<br />
<br />
<br />
===Genes===<br />
<br />
====Genes data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'genes' data class.<br />
<br />
====Genetic interaction table (gene_genetic_interactions_*.tsv)====<br />
The file reports the summary of gene-level genetic interactions in FlyBase. This data is computed from the allele-level genetic interaction data captured by FlyBase curators.<br />
<br />
The file includes information for Dmel genes only.<br />
<br />
Interactions involving any of the following kinds of allele are considered when the gene-level genetic interaction data is computed:<br />
<br />
* classical mutations<br />
* alleles carried on transgenic constructs<br />
* loss-of-function mutations<br />
* gain-of-function mutations<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Starting_gene(s)_symbol''' <br />
|Current FlyBase symbol of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Starting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Interacting_gene(s)_symbol'''<br />
|Current FlyBase symbol of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interacting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interaction_type''' <br />
|Type of interaction observed, either 'suppressible' or 'enhanceable'.<br />
|-<br />
|'''Publication_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if the same genetic interaction has been reported in multiple references, multiple rows will exist for that genetic interaction in the file.<br />
<br />
* 'suppressible' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are suppressed by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
* 'enhanceable' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are enhanced by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
''e.g.''<br />
<br />
Pten&emsp;FBgn0026379&emsp;Akt1&emsp;FBgn0010379&emsp;suppressible&emsp;FBrf0127089<br />
<br />
indicates that phenotype(s) caused by a mutation of Pten are suppressed by a mutation of Akt1.<br />
<br />
* For cases where multiple genes are simultaneously mutated in either (or both) the starting and interacting genotype, then the genes involved are separated by a '|' in the relevant columns. In this case, the order of the list of symbols and of the list of ids in columns 1 and 2, or in columns 3 and 4 respectively are the same, so that the FBgn corresponding to the symbol for each gene can easily be identified.<br />
<br />
''e.g.''<br />
<br />
robo1|sli&emsp;FBgn0005631|FBgn0264089&emsp;RhoGAP93B&emsp;FBgn0038853&emsp;enhanceable&emsp;FBrf0191476<br />
<br />
indicates that:<br />
* phenotype(s) caused by a robo1, sli double mutant combination are enhanced by a mutation of RhoGAP93B.<br />
* FBgn0005631 corresponds to robo1, FBgn0264089 corresponds to sli<br />
<br />
<br />
====RNA-Seq RPKM values (gene_rpkm_report_fb_*.tsv.gz)====<br />
This file reports gene expression values based on RNA-Seq experiments, calculated as reads per kilobase per million reads (RPKM). RPKM values are calculated only for the unique exonic regions of the gene (excluding segments that overlap other genes), except for genes derived from dicistronic/polycistronic transcripts, in which case all exon regions are used in the RPKM expression calculation.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Release_ID'''<br />
|The D. melanogaster annotation set version from which the gene model used in the analysis derives.<br />
|-<br />
|'''FBgn#'''<br />
|The unique FlyBase gene ID for this gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|The official FlyBase symbol for this gene.<br />
|-<br />
|'''Parent_library_FBlc#'''<br />
|The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''Parent_library_name'''<br />
|The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''RNASource_FBlc#'''<br />
|The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RNASource_name'''<br />
|The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RPKM_value'''<br />
|The RPKM expression value for the gene in the specified RNA-Seq experiment.<br />
|-<br />
|'''Bin_value'''<br />
|The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression).<br />
|-<br />
|'''Unique_exon_base_count'''<br />
|The number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts.<br />
|-<br />
|'''Total_exon_base_count'''<br />
|The number of bases in all exons of this gene.<br />
|-<br />
|'''Count_used'''<br />
|Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction table (physical_interactions_fb_*.tsv.gz)====<br />
This file reports unique gene pairs with curated support for some type of physical interaction. The file does not currently distinguish between genes that are involved in protein-protein or RNA-protein interactions (or both).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_FBgn1'''<br />
|The unique FlyBase gene ID for the first gene of the interacting pair.<br />
|-<br />
|'''gene_symbol1'''<br />
|The official FlyBase symbol for the first gene of the interacting pair.<br />
|-<br />
|'''gene_FBgn2'''<br />
|The unique FlyBase gene ID for the second gene of the interacting pair.<br />
|-<br />
|'''gene_symbol2'''<br />
|The official FlyBase symbol for the second gene of the interacting pair.<br />
|-<br />
|'''FBrf(s)'''<br />
|The unique FlyBase IDs for the publications supporting this interaction.<br />
|-<br />
|'''FBig_id'''<br />
|The unique FlyBase ID for this pairwise interaction.<br />
|-<br />
|'''#_reported_interactions'''<br />
|The number of distinct experiments in support of this interaction.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction MITAB file (physical_interactions_mitab_fb_*.tsv.gz)====<br />
This file reports each individual experiment curated by FlyBase that supports a physical interaction between two gene products. There can be multiple experiments (multiple rows in the file) between products of the same gene pair. Interaction molecule types currently curated are protein-protein, protein-RNA or RNA-RNA. <br />
<br />
This file is in PSI-MI TAB format, a tab-delimited format developed by the HUPO Proteomics Standards Initiative (PSI) Molecular Interactions (MI) working group to facilitate interactomics data comparison and exchange. Details on the general MITAB format can be found [https://psicquic.github.io/MITAB27Format.html here]. The file makes use of the Molecular Interactions ontology which can be searched or browsed [https://www.ebi.ac.uk/ols/ontologies/mi here]. Fields are filled with “-” if values are missing or not relevant.<br />
<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading<br />
!General format <br />
!FlyBase example<br />
!Content description<br />
|-<br />
|'''1'''<br />
|'''ID(s) Interactor A'''<br />
|database:identifier<br />
|flybase:FBgn0002121<br />
|The unique Flybase identifier for the first gene of the interacting pair.<br />
|-<br />
|'''2'''<br />
|'''ID(s) Interactor B'''<br />
|”<br />
|”<br />
|The unique Flybase identifier for the second gene of the interacting pair.<br />
|-<br />
|'''3'''<br />
|'''Alt ID(s) Interactor A'''<br />
|database:identifier<br />
|<nowiki>flybase:CG2671|entrez gene/locuslink:33156</nowiki><br />
|<nowiki>The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|”.</nowiki><br />
|-<br />
|'''4'''<br />
|'''Alt ID(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''5'''<br />
|'''Alias(es) Interactor A'''<br />
|database:name(alias type)<br />
|flybase:l(2)gl(gene name)<br />
|The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.<br />
|-<br />
|'''6'''<br />
|'''Alias(es) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''7'''<br />
|'''Interaction Detection Method(s)'''<br />
|ontology:identifier(method name)<br />
|psi-mi:"MI:0006"(anti bait coimmunoprecipitation)<br />
|The assay used to detect the interaction, taken from the psi-mi ontology.<br />
|-<br />
|'''8'''<br />
|'''Publication 1st Author(s)'''<br />
|surname initial(s) (publication year)<br />
|Betschinger K. (2003)<br />
|The first author and year of the publication where the interaction is described.<br />
|-<br />
|'''9'''<br />
|'''Publication ID(s)'''<br />
|database:identifier<br />
|<nowiki>flybase:FBrf0157155|pubmed:12629552</nowiki><br />
|<nowiki>The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.</nowiki><br />
|-<br />
|'''10'''<br />
|'''Taxid Interactor A'''<br />
|taxid:identifier<br />
|taxid:7227("Drosophila melanogaster")<br />
|The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.<br />
|-<br />
|'''11'''<br />
|'''Taxid Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''12'''<br />
|'''Interaction Type(s)'''<br />
|ontology:identifier(interaction type)<br />
|psi-mi:"MI:0915"(physical association)<br />
|Taken from the psi-mi ontology. Most often “physical association” for FlyBase.<br />
|-<br />
|'''13'''<br />
|'''Source Database(s)'''<br />
|ontology:identifier(database name)<br />
|psi-mi:"MI:0478"(flybase)<br />
|All interactions are curated by FlyBase.<br />
|-<br />
|'''14'''<br />
|'''Interaction Identifier(s)'''<br />
|database:identifier<br />
|flybase:FBrf0157155-13.coIP.WB<br />
|The unique FlyBase identifier for this interaction.<br />
|-<br />
|'''15'''<br />
|'''Confidence Value(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''16'''<br />
|'''Expansion Method(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''17'''<br />
|'''Biological Role(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''18'''<br />
|'''Biological Role(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''19'''<br />
|'''Experimental Role(s) Interactor A'''<br />
|ontology:identifier(experimental role name)<br />
|psi-mi:"MI:0496"(bait)<br />
|The role played by the interactor in the experiment. Taken from the psi-mi ontology.<br />
|-<br />
|'''20'''<br />
|'''Experimental Role(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''21'''<br />
|'''Type(s) Interactor A'''<br />
|ontology:identifier(interactor type name)<br />
|psi-mi:"MI:0326"(protein)<br />
|The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.<br />
|-<br />
|'''22'''<br />
|'''Type(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''23'''<br />
|'''Xref(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''24'''<br />
|'''Xref(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''25'''<br />
|'''Interaction Xref(s)'''<br />
|database:identifier<br />
|flybase:FBig0000000103<br />
|<nowiki>Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.</nowiki><br />
|-<br />
|'''26'''<br />
|'''Annotation(s) Interactor A'''<br />
|topic:text<br />
|isoform-comment:a isoform<br />
|Information on whether the interaction is specific to a particular interactor isoform.<br />
|-<br />
|'''27'''<br />
|'''Annotation(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''28'''<br />
|'''Interaction Annotation(s)'''<br />
|topic:text<br />
|molecular source:Source was cell extract of S2 cell line; bait produced from endogenous gene; prey produced from endogenous gene.|comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.<br />
|Describes the source(s) of the interaction participants and includes free text comments about the interaction.<br />
|-<br />
|'''29'''<br />
|'''Host Organism(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''30'''<br />
|'''Interaction Parameters'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''31'''<br />
|'''Creation Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''32'''<br />
|'''Update Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''33'''<br />
|'''Checksum Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''34'''<br />
|'''Checksum Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''35'''<br />
|'''Interaction Checksum'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''36'''<br />
|'''Negative'''<br />
|<br />
|FALSE<br />
|All interactions in FlyBase are positive.<br />
|-<br />
|'''37'''<br />
|'''Feature(s) Interactor A'''<br />
|feature_type:range(text)<br />
|sufficient binding region:aa 1-58(N-terminal region)<br />
|Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.<br />
|-<br />
|'''38'''<br />
|'''Feature(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''39'''<br />
|'''Stoichiometry Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''40'''<br />
|'''Stoichiometry Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''41'''<br />
|'''Identification Method(s) Participant A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''42'''<br />
|'''Identification Method(s) Participant B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|}<br />
<br />
<br />
====Functional complementation table (gene_functional_complementation_*.tsv)====<br />
<br />
This file reports when functional complementation of Dmel genes by non-Dmel orthologs has been observed. This data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature. The file contains a list of gene Dmel - to - non-Dmel-ortholog gene pairs where a transgenic construct/mutant allele of the non-Dmel ortholog has been shown to at least partially suppress mutant phenotype(s) of an allele of the Dmel gene.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''Dmel gene (symbol)'''<br />
|Current FlyBase symbol of Dmel gene.<br />
|-<br />
|'''2'''<br />
|'''Dmel gene (FBgn)'''<br />
|Current FlyBase identifier (FBgn#) of Dmel gene in column 1.<br />
|-<br />
|'''3'''<br />
|'''Functionally complementing ortholog (symbol)'''<br />
|Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''4'''<br />
|'''Functionally complementing ortholog (FBgn#)'''<br />
|Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''5'''<br />
|'''Supporting_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if multiple references support the same functional complementation statement, multiple rows will exist for that statement in the file.<br />
<br />
<br />
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====<br />
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, UniProtKB/SwissProt/TrEMBL protein accessions, NCBI Entrez gene IDs and NCBI RefSeq transcript and protein accessions associated with FlyBase genes.<br />
<br />
The file includes:<br />
* nuclear genes with sequence accession numbers<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes without sequence accession numbers<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''2'''<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''3'''<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''4'''<br />
|'''nucleotide_accession'''<br />
|EMBL/GenBank/DDBJ nucleotide accession associated with the gene.<br />
|-<br />
|'''5'''<br />
|'''na_based_protein_accession'''<br />
|EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column<br />
|-<br />
|'''6'''<br />
|'''UniprotKB/Swiss-Prot/TrEMBL_accession'''<br />
|UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.<br />
|-<br />
|'''7'''<br />
|'''EntrezGene_ID'''<br />
|NCBI Entrez ID associated with the gene.<br />
|-<br />
|'''8'''<br />
|'''RefSeq_transcripts'''<br />
|NCBI RefSeq transcript accession associated with the gene.<br />
|-<br />
|'''9'''<br />
|'''RefSeq_proteins'''<br />
|NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.<br />
<br />
* A single row contains '''only''' information about an EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession '''or''' an NCBI Entrez gene ID '''or''' an NCBI RefSeq transcript accession.<br />
<br />
* For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 4 ('nucleotide_accession'). If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 4, this protein accession is listed in column 5 ('na_based_protein_accession'). In this case, columns 6, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 6 ('UniprotKB/Swiss-Prot/TrEMBL_accession'). In this case, columns 4, 5, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI Entrez gene, an ID associated with the gene is listed in column 7 ('EntrezGene_ID'). In this case, columns 4, 5, 6, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI RefSeq accession, a transcript accession associated with the gene is listed in column 8 ('RefSeq_transcripts'). If there is also an NCBI RefSeq protein accession associated with that gene '''and''' with the transcript accession in column 8, this protein accession is listed in column 9 ('RefSeq_proteins'). In this case, columns 4, 5, 6 and 7 are always empty.<br />
<br />
<br />
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====<br />
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''secondary_FBgn#(s)'''<br />
|Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).<br />
|-<br />
|'''annotation_ID'''<br />
|Current annotation identifier associated with the gene.<br />
|-<br />
|'''secondary_annotation_ID(s)'''<br />
|Secondary annotation identifier(s) associated with the gene (comma separated values).<br />
|-<br />
|}<br />
Notes:<br />
<br />
* If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702). <br />
<br />
<br />
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====<br />
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.<br />
<br />
The file includes:<br />
* non-melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* ''D. melanogaster'' genes<br />
* non-melanogaster genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''gene_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GLEANR_ID'''<br />
|GLEANR identifier assigned by the AAA Consortium.<br />
|-<br />
|}<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====<br />
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.<br />
<br />
The file includes:<br />
* genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FlyBase_FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FlyBase_FBtr'''<br />
|Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.<br />
|-<br />
|'''FlyBase_FBpp'''<br />
|Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript and the polypeptide it encodes (if relevant). Thus if a gene encodes multiple isoforms, multiple rows with exist for that gene in the file.<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (expanded) (fbgn_fbtr_fbpp_expanded_*.tsv)====<br />
This expanded version of the "FBgn <=> FBtr <=> FBpp IDs" file adds organism, symbol and type information to the identifiers for sequence localized genes and their related transcript and protein products.<br />
<br />
The file includes:<br />
* sequence localized nuclear genes with transcript/polypeptide annotations.<br />
* sequence localized mitochondrial genes with transcript/polypeptide annotations.<br />
<br />
it excludes:<br />
* genes that have not been localized to the reference genome assembly for a given species.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''organism'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''2'''<br />
|'''gene_type'''<br />
|The type of gene, represented by a Sequence Ontology term. <br />
|-<br />
|'''3'''<br />
|'''gene_ID'''<br />
|Current "FBgn" identifier of gene.<br />
|-<br />
|'''4'''<br />
|'''gene_symbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|'''5'''<br />
|'''gene_fullname'''<br />
|Current full name of the gene.<br />
|-<br />
|'''6'''<br />
|'''annotation_ID'''<br />
|Current FlyBase annotation identifier of the gene.<br />
|-<br />
|'''7'''<br />
|'''transcript_type'''<br />
|The type of transcript, represented by a Sequence Ontology term.<br />
|-<br />
|'''8'''<br />
|'''transcript_ID'''<br />
|Current FlyBase annotation identifier of the transcript.<br />
|-<br />
|'''9'''<br />
|'''transcript_symbol'''<br />
|Current symbol of the transcript.<br />
|-<br />
|'''10'''<br />
|'''polypeptide_ID'''<br />
|Current FlyBase annotation identifier of the polypeptide.<br />
|-<br />
|'''11'''<br />
|'''polypeptide_symbol'''<br />
|Current symbol of the polypeptide.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript annotation, and if applicable, its associated polypeptide annotation.<br />
* Multiple rows may exist for a given gene in the file.<br />
* The "polypeptide_ID" and "polypeptide_symbol" columns are blank for non-mRNA transcript types.<br />
* For non-melanogaster annotations derived from NCBI Gnomon, some genes may be associated with a mix of coding and non-coding transcripts.<br />
* For D. melanogaster annotations, annotation IDs have a "CG" prefix for coding genes, or a "CR" prefix for non-protein-coding genes.<br />
* For non-melanogaster annotations, the annotation ID prefix varies by organism: "GD" for D. simulans ("Dsim"), "GF" for D. ananassae ("Dana"), "GA" for D. pseudoobscura ("Dpse") and "GJ" for D. virilis ("Dvir")<br />
<br />
====FBgn exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====<br />
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.<br />
<br />
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.<br />
<br />
The file includes the following '''Dmel''' genes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
Notes:<br />
<br />
* Each line of the file '''can contain many''' tab separated columns:<br />
<br />
* '''The first column of a line''' contains the valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] of a gene.<br />
* '''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.<br />
<br />
<br />
====FBgn exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====<br />
The file is generated from the location of Affy2 oligos exactly as [[FlyBase:FilesOverview#5.2.6|described for Affy1 oligos]] above.<br />
<br />
<br />
====Genes map table (gene_map_table_*.tsv)====<br />
The file reports available localization information for FlyBase genes.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''current_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBid'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''recombination_loc'''<br />
|recombination map location.<br />
|-<br />
|'''cytogenetic_loc'''<br />
|cytogenetic location.<br />
|-<br />
|'''sequence_loc'''<br />
|genomic location.<br />
|-<br />
|}<br />
<br />
<br />
====Automated gene summaries (automated_gene_summaries.tsv)====<br />
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|FlyBase ID. The Valid FlyBase identifier number for the gene.<br />
|-<br />
|'''-'''<br />
|The gene summary as a string of plain text.<br />
|-<br />
|}<br />
<br />
<br />
====Gene Snapshots (gene_snapshots_*.tsv)====<br />
The file contains in plain text the gene snapshot information visible on gene report pages.<br />
<br />
It includes only Dmel protein coding genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier number for the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase symbol of the gene.<br />
|-<br />
|'''GeneName'''<br />
|Current FlyBase name of the gene.<br />
|-<br />
|'''datestamp'''<br />
|Date on which the information was last reviewed.<br />
|-<br />
|'''gene_snapshot_text'''<br />
|Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such.<br />
|-<br />
|}<br />
<br />
<br />
====Unique protein isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their unique protein isoforms.<br />
<br />
The file includes:<br />
* melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* melanogaster genes not located to the sequence<br />
* non-melanogaster genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FB_gene_symbol'''<br />
|Current FlyBase gene symbol of the gene.<br />
|-<br />
|'''representative_protein'''<br />
|Current FlyBase protein symbol of the representative protein isoform.<br />
|-<br />
|'''identical_protein(s)'''<br />
|Current FlyBase protein symbol(s) of identical protein isoforms.<br />
|-<br />
|}<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster, D. ananassae, D. pseudoobscura pseudoobscura, D. simulans and D. virilis (i.e. those with gene models supported by FlyBase) in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Gene Ontology annotation files (go)===<br />
====Gene Association File - GAF (gene_association.fb.gz)====<br />
<br />
The file contains the [http://www.geneontology.org/ Gene Ontology] (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.<br />
<br />
The file includes the following Dmel genes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
The columns of the file are described in [[FlyBase:Gene Ontology (GO) Annotation|section G.3.1.]] of the Reference manual.<br />
<br />
====Gene to Protein file (gp2protein.fb.gz)====<br />
<br />
<br />
The mapping file, gp2protein.fb, contains a full set of D.melanogaster protein coding genes localized to the genome mapped to UniProtKB protein identifiers.<br />
<br />
<br />
To minimise redundancy, where there are multiple UniProtKB accessions for an FBgn, where a Swiss-Prot accession exists, this is used. Otherwise all TrEMBLs are listed. Multiple UniProtKB accessions are separated using a semi-colon.<br />
<br />
<br />
Example format:<br />
FB:FBgn0086681 UniProtKB:Q0GYU3;UniProtKB:Q8INX4<br />
<br />
<br />
<br />
===Gene groups===<br />
====Gene group data (gene_group_data_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with their hierarchical relationships (where relevant) and member genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''Parent_FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Parent_FB_group_symbol'''<br />
|Current FlyBase symbol of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Group_member_FB_gene_id'''<br />
|Current FlyBase identifier (FBgn##) of member gene (if terminal group).<br />
|-<br />
|'''Group_member_FB_gene_symbol'''<br />
|Current FlyBase symbol of member gene (if terminal group).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Where groups are arranged into hierarchies:<br />
** the member genes are only associated with the terminal subgroups,<br />
** the immediate parent of any subgroup is identified in the ‘Parent_FB_group_id' and 'Parent_FB_group_symbol' columns.<br />
<br />
* Separate lines are used for each member gene, meaning that each terminal group is listed multiple times (equal to the number of member genes).<br />
<br />
<br />
====Gene groups with HGNC IDs (gene_groups_HGNC_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with the corresponding HGNC 'gene family' ID (where relevant).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''HGNC_family_ID'''<br />
|HGNC ID of equivalent human 'gene family'.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* The absence of an HGNC_family_ID entry indicates there is no equivalent HGNC gene family for that FlyBase gene group.<br />
<br />
* Because of different sub-group structures (etc), a single HGNC family may be associated with multiple FlyBase gene groups.<br />
<br />
* Similarly, a single FlyBase gene group may be associated with multiple HGNC gene families - these are shown on separate lines.<br />
<br />
<br />
===Alleles and Stocks===<br />
====Allele data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'alleles' data class.<br />
<br />
<br />
====Stock data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'stocks' data class.<br />
<br />
<br />
====Stock data (stocks_*.tsv.gz)====<br />
This file reports genetic components and related information about Stocks in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
!Example<br />
|-<br />
|'''FBst'''<br />
|The unique identifier assigned to this stock by FlyBase.<br />
|FBst0000002<br />
|-<br />
|'''collection_short_name'''<br />
|A short name for the stock collection that holds the stock.<br />
|Bloomington<br />
|-<br />
|'''stock_type_cv'''<br />
|The controlled vocabulary term and unique identifier that describe the state of the stock.<br />
|living stock ; FBsv:0000002<br />
|-<br />
|'''species'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of the stock.<br />
|Dmel<br />
|-<br />
|'''FB_genotype'''<br />
|Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.<br />
|w[*]; betaTub60D[2] Kr[If-1]/CyO<br />
|-<br />
|'''description'''<br />
|Genetic components of the stock as provided to FlyBase by the collection that holds the stock.<br />
|FlyTrap: ZCL1796 III<br />
|-<br />
|'''stock_number'''<br />
|The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.<br />
|110818<br />
|-<br />
|}<br />
<br />
<br />
====Genetic interactions (allele_genetic_interactions_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''interaction'''<br />
|Interaction information associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single interaction from a single reference. Thus if multiple genetic interactions have been reported for a given allele, or if multiple references report the same interaction for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
====Phenotypic data (allele_phenotypic_data_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''phenotype'''<br />
|Phenotypic data associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes: <br />
<br />
* Each row contains information about a single phenotype from a single reference. Thus if multiple phenotypes have been reported for a given allele, or if multiple references report the same phenotype for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
====Alleles <=> Genes (fbal_to_fbgn_fb_*.tsv)====<br />
This file reports the relationship between gene identifiers and the identifiers used for alleles of these genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''AlleleID'''<br />
|Current FlyBase identifier (FBal#) of the allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current symbol of the allele.<br />
|-<br />
|'''GeneID'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|}<br />
<br />
<br />
===Homologs===<br />
<br />
====Drosophila Orthologs (dmel_orthologs_in_drosophila_species_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their orthologs in other sequenced Drosophila genomes, as determined by OrthoDB. (The version of OrthoDB currently being used is shown in the 'Orthologs' -> 'Orthologs (via OrthoDB)' section of a Gene Report.)<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Ortholog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_Arm/Scaffold'''<br />
|Arm upon which the non-melanogaster orthologous gene is localized.<br />
|-<br />
|'''Ortholog_Location'''<br />
|Location of non-melanogaster orthologous gene on the arm.<br />
|-<br />
|'''Ortholog_Strand'''<br />
|Strand of non-melanogaster orthologous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''OrthoDB_Group_ID'''<br />
|OrthoDB orthology group ID to which the pair-wise association belongs.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association between a ''D. melanogaster'' gene and a non-melanogaster ortholog. Thus, multiple rows exist for each ''D. melanogaster'' gene in the file.<br />
<br />
====Drosophila Paralogs (dmel_paralogs_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their paralogs, as provided by DIOPT. (The version of DIOPT currently being used is shown in the 'Paralogs' -> 'Paralogs (via DIOPT)' section of a Gene Report.)<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Paralog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the paralogous gene.<br />
|-<br />
|'''Paralog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the paralogous gene.<br />
|-<br />
|'''Paralog_Arm/Scaffold'''<br />
|Arm upon which the paralogous gene is localized.<br />
|-<br />
|'''Paralog_Location'''<br />
|Location of paralogous gene on the arm.<br />
|-<br />
|'''Paralog_Strand'''<br />
|Strand of paralogous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for the paralog call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association between a given ''D. melanogaster'' and a paralog. Thus, two rows exist for each paralogous pair in the file.<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dmel_gene_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Dmel_gene_symbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Human_gene_HGNC_ID'''<br />
|HGNC ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_OMIM_ID'''<br />
|OMIM ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_symbol'''<br />
|HGNC gene symbol of orthologous human gene.<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|'''OMIM_Phenotype_IDs'''<br />
|OMIM Phenotype ID of orthologous human gene (comma separated values).<br />
|-<br />
|'''OMIM_Phenotype_IDs[name]'''<br />
|OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets). Multiple phenotype[name] entries are separated by a comma.<br />
|-<br />
|}<br />
<br />
===Human disease===<br />
<br />
====Human disease model data (disease_model_annotations_fb_*.tsv.gz)====<br />
This file reports (i) all experimental-based disease model annotations, associated with alleles; and (ii) all 'potential' disease models based on orthology to human disease genes in OMIM (see [http://flybase.org/reports/FBrf0241599 FBrf0241599] for more information on this pipeline) for ''D. melanogaster''. 'Alleles' encompass both classical alleles and transgenic alleles; the latter may relate to transgenic constructs of ''D. melanogaster'' genes or non-''D. melanogaster'' genes (often human genes) inserted into the ''D. melanogaster'' genome. These disease model annotations are reported in the "Human Disease Model Data" -> "Disease Ontology (DO) Annotations" section of the Gene and Allele Reports.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn ID'''<br />
|Current FlyBase identifier (FBgn#) of the gene associated with the allele of an experimental annotation, or the D. melanogaster ortholog of a human gene associated with a disease in OMIM.<br />
|-<br />
|'''Gene symbol'''<br />
|Current FlyBase symbol of the gene in column 1.<br />
|-<br />
|'''HGNC ID'''<br />
|HGNC ID of the gene identified in column 1 where it is a human gene (experimental-based annotations only).<br />
|-<br />
|'''DO qualifier'''<br />
|Type of association between the object of annotation and the disease - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.<br />
|-<br />
|'''DO ID'''<br />
|Disease Ontology (DO) ID.<br />
|-<br />
|'''DO term'''<br />
|Disease Ontology (DO) term.<br />
|-<br />
|'''Allele used in model (FBal ID)'''<br />
|Current FlyBase identifier (FBal#) of allele (experimental-based annotations only).<br />
|-<br />
|'''Allele used in model (symbol)'''<br />
|Current FlyBase symbol of allele (experimental-based annotations only).<br />
|-<br />
|'''Based on orthology with (HGNC ID)'''<br />
|HGNC ID of the human ortholog used for annotations based on orthology to human disease genes.<br />
|-<br />
|'''Based on orthology with (symbol)'''<br />
|HGNC gene symbol of the human ortholog used for annotations based on orthology to human disease genes.<br />
|-<br />
|'''Evidence/interacting alleles'''<br />
|Evidence code, with interacting allele(s) where appropriate. For experimental-based annotations, the evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma. For orthology-based annotations, the evidence code is 'inferred from electronic annotation'.<br />
|-<br />
|'''Reference (FBrf ID)'''<br />
|Current FlyBase identifier (FBrf#) of the source publication.<br />
|-<br />
|}<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
This is identical to the file of the same name listed under the 'Orthologs' section above.<br />
<br />
===Nomenclature===<br />
<br />
====Species abbreviation list (species-ab.gz)====<br />
<br />
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.<br />
<br />
There are 8 columns of data in the file, each separated by " | ".<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Internal_id'''<br />
|The Primary [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the organism.<br />
|-<br />
|'''Taxgroup'''<br />
|A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".<br />
|-<br />
|'''Abbreviation'''<br />
|The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.<br />
|-<br />
|'''Genus'''<br />
|The genus name of the organism.<br />
|-<br />
|'''Species name'''<br />
|The species name of the organism.<br />
|-<br />
|'''Common name'''<br />
|The common name of the organism. This column may be blank.<br />
|-<br />
|'''Comment'''<br />
|A free text field for additional comments. This column may be blank.<br />
|-<br />
|'''Ncbi-taxon-id'''<br />
|The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.<br />
|-<br />
|}<br />
<br />
An html version of this file is also available - see the [[FlyBase:Abbreviations|Species Abbreviations]] page.<br />
<br />
<br />
<br />
===Ontology Terms===<br />
<br />
The [http://{{flybaseorg}}/static_pages/docs/refman/refman-G.html#G.2. ontology files] used by FlyBase are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and may be viewed using the free [http://www.oboedit.org/ OBO-Edit] tool.<br />
<br />
Ontologies undergo continual development. Links are provided to the 'frozen versions' used for the current release of FlyBase, together with links to the current 'live' versions at external sites.<br />
<br />
====Frozen files used for this release of FlyBase====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
* FBdv: fly_development<br />
* FBcv: flybase controlled vocabulary<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
====Current 'Live' Files====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_anatomy.obo' version''<br />
* FBdv: fly_development<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_development.obo' version''<br />
* FBcv: flybase controlled vocabulary<br />
''Note: link points to the ontology version fbcv-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'flybase_controlled_vocabulary.obo' version''<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
===Genomes: Annotation and Sequence===<br />
====All Sequenced Drosophila Species====<br />
<br />
Links are available to the following FTP repositories:<br />
<br />
* Current FTP repository<br />
* Current FastA repository<br />
* Current GFF repository<br />
<br />
* FTP archive (previous releases)<br />
<br />
* Current list of individual FASTA files<br />
* Current list of individual GFF files<br />
<br />
<br />
====Individual Sequenced Drosophila Species====<br />
<br />
For release FB2018_06 onward, the above links are available for the following sequenced Drosophila species:<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila melanogaster<br />
|Dmel<br />
|-<br />
|Drosophila ananassae<br />
|Dana<br />
|-<br />
|Drosophila pseudoobscura pseudoobscura<br />
|Dpse<br />
|-<br />
|Drosophila simulans<br />
|Dsim<br />
|-<br />
|Drosophila virilis<br />
|Dvir<br />
|-<br />
|}<br />
<br />
<br />
For earlier archived releases, the above links are also available for these additional species (other members of the original 12 sequenced Drosophila species):<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila erecta<br />
|Dere<br />
|-<br />
|Drosophila grimshawi<br />
|Dgri<br />
|-<br />
|Drosophila mojavensis<br />
|Dmoj<br />
|-<br />
|Drosophila persimilis<br />
|Dper<br />
|-<br />
|Drosophila sechellia<br />
|Dsec<br />
|-<br />
|Drosophila willistoni<br />
|Dwil<br />
|-<br />
|Drosophila yakuba<br />
|Dyak<br />
|-<br />
|}<br />
<br />
====FASTA files====<br />
<br />
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:<br />
<br />
'''dmel-all-<data type>-r<release-number>.fasta.gz'''<br />
<br />
or<br />
<br />
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''<br />
<br />
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome. <br />
<br />
{| class= "wikitable"<br />
!Data Type <br />
!Content Description<br />
|-<br />
|'''aligned ''' <br />
|The region of genomic sequence that analysis features align to.<br />
|-<br />
|'''CDS''' <br />
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.<br />
|-<br />
|'''chromosome'''<br />
|The sequence of each chromosome arm.<br />
|-<br />
|'''clones''' <br />
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.<br />
|-<br />
|'''exon ''' <br />
|The sequence of each exon split up into individual FASTA records.<br />
|-<br />
|'''five_prime_UTR'''<br />
|The sequence of 5' untranslated regions.<br />
|-<br />
|'''gene''' <br />
|The sequence of the gene span.<br />
|-<br />
|'''gene_extended2000''' <br />
|The sequence of the gene span with 2000 base pairs added upstream and downstream.<br />
|-<br />
|'''intergenic'''<br />
|The sequence of chromosomal regions between genes that do not contain known gene models.<br />
|-<br />
|'''intron''' <br />
|The sequence of each intron split up into individual FASTA records.<br />
|-<br />
|'''miRNA''' <br />
|The sequence of transcripts that are typed as micro RNAs.<br />
|-<br />
|'''miscRNA''' <br />
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.<br />
|-<br />
|'''ncRNA''' <br />
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).<br />
|-<br />
|'''predicted''' <br />
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.<br />
|-<br />
|'''pseudogene''' <br />
|The sequence of transcripts that are typed as pseudogenes.<br />
|-<br />
|'''sequence_features''' <br />
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.<br />
|-<br />
|'''synteny'''<br />
|The sequence of syntenic regions between two species.<br />
|-<br />
|'''three_prime_UTR'''<br />
|The sequence of 3' untranslated regions.<br />
|-<br />
|'''transcript'''<br />
|The sequence of transcripts that are typed as messenger RNAs (mRNA).<br />
|-<br />
|'''translation''' <br />
|The resulting protein sequence from protein coding transcripts.<br />
|-<br />
|'''transposon'''<br />
|The sequence of transposable elements.<br />
|-<br />
|'''tRNA''' <br />
|The sequence of transcripts that are typed as transfer RNAs (tRNA).<br />
|}<br />
<br />
<br />
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format<br />
<br />
'''field_name=value;'''<br />
<br />
Multiple field values are separated by commas<br />
<br />
'''field_name=value1,value2;'''<br />
<br />
This table describes some of the field names found in our FASTA headers <br />
<br />
{|class = "wikitable"<br />
<br />
!Field Name<br />
!Description<br />
|-<br />
|'''type''' <br />
|The feature type of the FASTA sequence record.<br />
|-<br />
|'''loc''' <br />
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.<br />
|-<br />
|'''ID''' <br />
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.<br />
|-<br />
|'''name'''<br />
|The name or symbol of the feature.<br />
|-<br />
|'''dbxref'''<br />
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.<br />
|-<br />
|'''MD5'''<br />
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.<br />
|-<br />
|'''length'''<br />
|The length of the sequence found in the FASTA record.<br />
|-<br />
|'''release'''<br />
|The release number denotes the annotation release which this FASTA record corresponds to.<br />
|-<br />
|'''species'''<br />
|The species abbreviation that this FASTA record corresponds to.<br />
|}<br />
<br />
<br />
====GFF files====<br />
<br />
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features.<br />
<br />
For melanogaster, there are 3 GFF files distributed, they include:<br />
<br />
:'''dmel-all-r<release-number>.gff.gz'''<br />
::Contains all chromosome arms<br />
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''<br />
::Same as above except all match and match_part features have been removed<br />
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''<br />
::Contains only a single chromosome arm as identifed by the filename<br />
<br />
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues. <br />
<br />
The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gff/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gff/<br />
<br />
<br />
====GTF files====<br />
<br />
The FlyBase GTF files follow the [http://mblab.wustl.edu/GTF22.html GTF v2.2] specification. The GTF files contain feature line definitions for gene models.<br />
<br />
The GTF are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gtf/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gtf/<br />
<br />
<br />
===Transcripts and Polypeptides===<br />
<br />
====Transcript data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'transcripts' data class.<br />
<br />
<br />
====Polypeptide data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'polypeptide' data class.<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster, D. ananassae, D. pseudoobscura pseudoobscura, D. simulans and D. virilis (i.e. those with gene models supported by FlyBase) in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Transposons, Transgenic Constructs, and Insertions===<br />
<br />
====Insertions (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'insertions' data class.<br />
<br />
<br />
====Transgenic Constructs (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'transgenic constructs' data class.<br />
<br />
<br />
====Transgenic construct maps (construct_maps.zip)====<br />
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the respective recombinant construct or transgenic transposon.<br />
<br />
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.<br />
<br />
<br />
====Map data for insertions (insertion_mapping_*.tsv)====<br />
The insertion mapping table reports available localization information for '''Dmel''' insertions.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''insertion_symbol'''<br />
|Current symbol of insertion.<br />
|-<br />
|'''FBti#'''<br />
|Current FlyBase identifier (FBti#) of insertion<br />
.<br />
|-<br />
|'''genomic_location'''<br />
|Genomic location of insertion.<br />
|-<br />
|'''range'''<br />
|Range (t/f) indicates whether genomic location is range or single base.<br />
|-<br />
|'''orientation'''<br />
|Orientation (1/0) indicates orientation of insertion on chromosome.<br />
|-<br />
|'''estimated_cytogenetic_location'''<br />
|Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.<br />
|-<br />
|'''observed_cytogenetic_location'''<br />
|Observed cytogenetic location reported in the literature.<br />
|-<br />
|}<br />
<br />
<br />
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====<br />
This is a file of 'canonical' sequences of transposable elements of Drosophila species (primarily but not exclusively of D. melanogaster), including the protein sequences of encoded genes. Based on a file originally compiled by Michael Ashburner; currently maintained by Casey Bergman.<br />
<br />
The record for each element starts with a line prefixed by "ID" and ends with a line containing "//". The sequence data are in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL/GenBank/DDBJ format]; included for each entry is the FlyBase natural TE identifier (FBtennnnnnn) and notes on original source(s).<br />
<br />
====Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json.gz)====<br />
This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the [https://bdsc.indiana.edu/ Bloomington Drosophila Stock Center], in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format [http://flybase.org/GAL4/freq_used_drivers.tsv here].<br />
<br />
===Aberrations===<br />
====Aberration data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'aberrations' data class.<br />
<br />
<br />
====Balancer data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'balancers' data class.<br />
<br />
<br />
===Large dataset metadata===<br />
====Dataset metadata members (dataset_metadata_fb_*.tsv.gz)====<br />
This file lists all features that are associated with a dataset/collection (e.g., genes, cDNA clones, TF_binding_sites, Affymetrix probes).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dataset_Metadata_ID'''<br />
|The unique FlyBase ID for the dataset.<br />
|-<br />
|'''Dataset_Metadata_Name'''<br />
|The official FlyBase symbol for the dataset.<br />
|-<br />
|'''Item_ID'''<br />
|The unique FlyBase ID for the feature associated with this dataset.<br />
|-<br />
|'''Item_Name'''<br />
|The official FlyBase symbol for the feature associated with this dataset.<br />
|-<br />
|}<br />
<br />
<br />
===Clones===<br />
<br />
====Clone data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'clones' data class.<br />
<br />
<br />
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====<br />
The file reports basic cDNA clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of cDNA clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''dataset_metadata_name'''<br />
|Name of dataset associated with clone.<br />
|-<br />
|'''cDNA_accession(s)'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|'''EST_accession(s)'''<br />
|EMBL/GenBank/DDBJ EST accession number.<br />
|-<br />
|}<br />
<br />
<br />
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====<br />
<br />
The file reports basic genomic clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of genomic clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''accession'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|}<br />
<br />
<br />
===References===<br />
====Combined reference data (Chado XML)====<br />
The chado XML file generated from the FlyBase PostgreSQL database for the 'references' data class.<br />
<br />
<br />
====FlyBase FBrf <=> PubMed ID <=> PMCID <=> DOI (fbrf_pmid_pmcid_doi_fb_*.tsv.gz)====<br />
<br />
This file lists all publications in the FlyBase bibliography that have a PubMed ID. Additional identifiers are listed as applicable.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBrf'''<br />
|The unique FlyBase ID for this publication.<br />
|-<br />
|'''PMID'''<br />
|The unique PubMed ID for this publication.<br />
|-<br />
|'''PMCID'''<br />
|The unique PubMed Central ID for this publication, if applicable.<br />
|-<br />
|'''DOI'''<br />
|The digital object identifier assigned to the publication.<br />
|-<br />
|'''pub_type'''<br />
|The publication type (for example, paper, review, erratum, abstract, book, etc.)<br />
|-<br />
|'''miniref'''<br />
|A short citation listing the first author, year of publication, journal, volume, issue and page numbers.<br />
|-<br />
|'''pmid_added'''<br />
|The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.<br />
|-<br />
|}<br />
<br />
<br />
===Map conversion tables===<br />
====Cytological <=> Sequence (genome-cyto-seq.txt)====<br />
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [[FlyBase:Computed_cytological_data|section G.5.1.]] of the Reference manual.<br />
<br />
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.<br />
<br />
The columns in the file are:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|Cytogenetic map position as described by Bridges.<br />
|-<br />
|'''-'''<br />
|First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|'''-'''<br />
|Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Cytological <=> Genetic (cytotable.txt)====<br />
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.<br />
<br />
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.<br />
<br />
<br />
====Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)====<br />
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 6 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Cytogenetic map position'''<br />
|Cytogenetic map position.<br />
|-<br />
|'''Genetic map position'''<br />
|Genetic map position.<br />
|-<br />
|'''Sequence coordinates (release 6)'''<br />
|Sequence coordinates (release 6) for the interval.<br />
|-<br />
|'''R6 conversion notes'''<br />
|<br />
|-<br />
|}<br />
<br />
<br />
An html version of this file is also available - see the [http://{{flybaseorg}}/static_pages/docs/cytotable3.html Map Conversion Table] page.<br />
<br />
<br />
====Genes map table (gene_map_table_fb_*.tsv)====<br />
This is identical to the file listed under the genes section above.<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=170649FlyBase:QuickSearch2019-12-20T18:59:00Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Homologs tab| Homologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
<br />
All tabs search data for all species included in FlyBase. An option to filter by species is provided in the resulting hit-list.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://{{flybaseorg}}/vocabularies Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from all data classes of reports.<br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [[FlyBase:RNA-Seq Overview | RNA-Seq overview page]]. There are '''video tutorials''' available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern, or gene promoter expression pattern, as curated from the literature.<br />
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'''Search by curated expression pattern''' Click the option "'''by curated expression pattern'''". Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. Please note that you must fill either the '''Developmental Stage''' or '''Anatomy or Cell Type''' boxes to use this search option; you cannot fill only the '''Cellular Component''' box. Please note that you must use a valid controlled vocabulary term, and cannot search using a synonym. Synonyms will fail to autocomplete; you will instead see text reading "...no matching text suggestions...", and your query will produce no matches. You can use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to search with your synonym to find a valid Controlled Vocabulary term.<br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled; you do, however, need to also fill the '''Developmental Stage''' box in this case. Sex-specific queries use the '''qualifier''' box for '''Developmental Stage'''. You must fill the '''Developmental Stage''' box to use a [http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000332 sex qualifier], even if you have filled the '''Anatomy/Cell Type''' box.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled, as only a small subset of expression pattern curation for driver or reporter alleles include a GO cellular component term, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=&id=GO:0043195 terminal bouton]. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''by curated expression pattern''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Expression terms''' column of the '''GAL4 etc''' hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Search by expression pattern of a particular gene''' Click the option "'''reflecting expression pattern of a particular gene'''". The form has one input box, '''Gene'''. You can enter either a valid FlyBase gene symbol, such as [http://{{flybaseorg}}/reports/FBgn0000490 dpp], or a valid FlyBase gene ID number, such as FBgn0000490; synonyms or full gene names will not work in this search. Please note that this search is only for drivers and/or reporters that have been curated as reflecting the expression pattern of a specific gene; this search will not find drivers/reporters with an expression pattern similar to that of the gene you have entered in the search box, nor will it find drivers/reporters that are associated with a specific gene, but have not been curated as reflecting expression of that gene. Please note: this search option is an alternative to the "'''by curated expression pattern'''" search option; you can choose only one of these two options.<br />
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'''Output format options''' IN PROGRESS Examples of how to manipulate the results page can be found in this [http://{{flybaseorg}}/commentaries/2019_08/GAL4TabUpgrade.html FlyBase commentary] Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for. Clicking through to the '''Allele Reports''', '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===Pathways tab===<br />
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This tab searches FlyBase-curated 'Pathway Reports' - sets of genes/gene products that have been experimentally shown to act within a pathway or to regulate a pathway.<br />
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To use, either start typing and select the appropriate Pathway Report name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Pathway Reports that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Pathway Reports to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Pathway Reports.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Note, as the GO is an ontology, all child terms will possess the property of the parent, therefore consider using '''Records annotated with this term OR any of its CHILDREN TERMS''' to get a complete gene list.<br />
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Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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'''You can search by disease using:'''<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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'''You can search by human disease-associated gene using:'''<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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'''You can search by ''Drosophila melanogaster'' gene using:'''<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
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'''The QuickSearch auto-completion feature is active in this tab; auto-completion works for''' <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Homologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. It can also be used to find paralogs within ''D. melanogaster'', as provided by DIOPT. The DIOPT dataset integrates ortholog/paralog predictions for humans and 9 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa. A related '''video tutorial''' can be found at [https://www.youtube.com/watch?v=JsNyrNG28M0 Using the Orthology search tool].<br />
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To search for orthologs, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset).<br />
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To search for paralogs within ''D. melanogaster'', choose the DIOPT dataset and select ''D. melanogaster'' as '''both''' the input and output species.<br />
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Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''A. thaliana'' || [https://apps.araport.org/thalemine/keywordSearchResults.do?searchTerm= Araport] gene symbol (e.g. CDC2) or gene ID (e.g. AT3G48750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 824036)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog/paralog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given gene-pair relationship compared to the total number of tools that compute relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given gene has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given gene in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''Align''': link to an alignment between the given gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs/paralogs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''gene''': official gene symbol, as used in the relevant model organism database<br />
* '''gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given gene has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given gene in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any pairwise calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
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This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
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The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=170574FlyBase:QuickSearch2019-08-22T18:49:31Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Homologs tab| Homologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
<br />
All tabs search data for all species included in FlyBase. An option to filter by species is provided in the resulting hit-list.<br />
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===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://{{flybaseorg}}/vocabularies Vocabularies]" button above the QuickSearch box on the home page.<br />
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===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from all data classes of reports.<br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [[FlyBase:RNA-Seq Overview | RNA-Seq overview page]]. There are '''video tutorials''' available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern, or gene promoter expression pattern, as curated from the literature.<br />
<br />
'''Search by curated expression pattern''' Click the option "'''by curated expression pattern'''". Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. Please note that you must fill either the '''Developmental Stage''' or '''Anatomy or Cell Type''' boxes to use this search option; you cannot fill only the '''Cellular Component''' box. Please note that you must use a valid controlled vocabulary term, and cannot search using a synonym. Synonyms will fail to autocomplete; you will instead see text reading "...no matching text suggestions...", and your query will produce no matches. You can use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to search with your synonym to find a valid Controlled Vocabulary term.<br />
<br />
'''Search with qualifier terms ''' THIS FEATURE HAS BEEN TEMPORARILY DISABLED. You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled; you do, however, need to also fill the '''Developmental Stage''' box in this case. Sex-specific queries use the '''qualifier''' box for '''Developmental Stage'''. You don't need to fill '''Developmental Stage''' box to use a [http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000332 sex qualifier], but must fill '''Anatomy/Cell Type''' box if you leave '''Developmental Stage''' unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled, as only a small subset of expression pattern curation for driver or reporter alleles include a GO cellular component term, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=&id=GO:0043195 terminal bouton]. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''by curated expression pattern''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Expression terms''' column of the '''GAL4 etc''' hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Search by expression pattern of a particular gene''' Click the option "'''reflecting expression pattern of a particular gene'''". The form has one input box, '''Gene'''. You can enter either a valid FlyBase gene symbol, such as [http://{{flybaseorg}}/reports/FBgn0000490 dpp], or a valid FlyBase gene ID number, such as FBgn0000490; synonyms or full gene names will not work in this search. Please note that this search is only for drivers and/or reporters that have been curated as reflecting the expression pattern of a specific gene; this search will not find drivers/reporters with an expression pattern similar to that of the gene you have entered in the search box, nor will it find drivers/reporters that are associated with a specific gene, but have not been curated as reflecting expression of that gene. Please note: this search option is an alternative to the "'''by curated expression pattern'''" search option; you can choose only one of these two options.<br />
<br />
'''Output format options''' IN PROGRESS Examples of how to manipulate the results page can be found in this [http://{{flybaseorg}}/commentaries/2019_08/GAL4TabUpgrade.html FlyBase commentary] Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for. Clicking through to the '''Allele Reports''', '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===Pathways tab===<br />
<br />
This tab searches FlyBase-curated 'Pathway Reports' - sets of genes/gene products that have been experimentally shown to act within a pathway or to regulate a pathway.<br />
<br />
To use, either start typing and select the appropriate Pathway Report name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Pathway Reports that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Pathway Reports to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Pathway Reports.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Note, as the GO is an ontology, all child terms will possess the property of the parent, therefore consider using '''Records annotated with this term OR any of its CHILDREN TERMS''' to get a complete gene list.<br />
<br />
Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
'''You can search by disease using:'''<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
'''You can search by human disease-associated gene using:'''<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
'''You can search by ''Drosophila melanogaster'' gene using:'''<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
'''The QuickSearch auto-completion feature is active in this tab; auto-completion works for''' <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Homologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. It can also be used to find paralogs within ''D. melanogaster'', as provided by DIOPT. The DIOPT dataset integrates ortholog/paralog predictions for humans and 9 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa. A related '''video tutorial''' can be found at [https://www.youtube.com/watch?v=JsNyrNG28M0 Using the Orthology search tool].<br />
<br />
To search for orthologs, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset).<br />
<br />
To search for paralogs within ''D. melanogaster'', choose the DIOPT dataset and select ''D. melanogaster'' as '''both''' the input and output species.<br />
<br />
Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''A. thaliana'' || [https://apps.araport.org/thalemine/keywordSearchResults.do?searchTerm= Araport] gene symbol (e.g. CDC2) or gene ID (e.g. AT3G48750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 824036)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog/paralog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given gene-pair relationship compared to the total number of tools that compute relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given gene has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given gene in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''Align''': link to an alignment between the given gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs/paralogs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''gene''': official gene symbol, as used in the relevant model organism database<br />
* '''gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given gene has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given gene in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any pairwise calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=170569FlyBase:QuickSearch2019-08-21T20:47:22Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Homologs tab| Homologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
<br />
All tabs search data for all species included in FlyBase. An option to filter by species is provided in the resulting hit-list.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://{{flybaseorg}}/vocabularies Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from all data classes of reports.<br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [[FlyBase:RNA-Seq Overview | RNA-Seq overview page]]. There are '''video tutorials''' available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern, or gene promoter expression pattern, as curated from the literature.<br />
<br />
'''Search by curated expression pattern''' Click the option "'''by curated expression pattern'''". Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. Please note that you must fill either the '''Developmental Stage''' or '''Anatomy or Cell Type''' boxes to use this search option; you cannot fill only the '''Cellular Component''' box. Please note that you must use a valid controlled vocabulary term, and cannot search using a synonym. Synonyms will fail to autocomplete; you will instead see text reading "...no matching text suggestions...", and your query will produce no matches. You can use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to search with your synonym to find a valid Controlled Vocabulary term.<br />
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'''Search with qualifier terms ''' THIS FEATURE HAS BEEN TEMPORARILY DISABLED. You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled; you do, however, need to also fill the '''Developmental Stage''' box in this case. Sex-specific queries use the '''qualifier''' box for '''Developmental Stage'''. You don't need to fill '''Developmental Stage''' box to use a [http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000332 sex qualifier], but must fill '''Anatomy/Cell Type''' box if you leave '''Developmental Stage''' unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled, as only a small subset of expression pattern curation for driver or reporter alleles include a GO cellular component term, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=&id=GO:0043195 terminal bouton]. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''by curated expression pattern''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Expression terms''' column of the '''GAL4 etc''' hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Search by expression pattern of a particular gene''' Click the option "'''reflecting expression pattern of a particular gene'''". The form has one input box, '''Gene'''. You can enter either a valid FlyBase gene symbol, such as [http://{{flybaseorg}}/reports/FBgn0000490 dpp], or a valid FlyBase gene ID number, such as FBgn0000490; synonyms or full gene names will not work in this search. Please note that this search is only for drivers and/or reporters that have been curated as reflecting the expression pattern of a specific gene; this search will not find drivers/reporters with an expression pattern similar to that of the gene you have entered in the search box, nor will it find drivers/reporters that are associated with a specific gene, but have not been curated as reflecting expression of that gene. Please note: this search option is an alternative to the "'''by curated expression pattern'''" search option; you can choose only one of these two options.<br />
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IN PROGRESS'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for. Clicking through to the '''Allele Reports''', '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===Pathways tab===<br />
<br />
This tab searches FlyBase-curated 'Pathway Reports' - sets of genes/gene products that have been experimentally shown to act within a pathway or to regulate a pathway.<br />
<br />
To use, either start typing and select the appropriate Pathway Report name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Pathway Reports that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Pathway Reports to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Pathway Reports.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Note, as the GO is an ontology, all child terms will possess the property of the parent, therefore consider using '''Records annotated with this term OR any of its CHILDREN TERMS''' to get a complete gene list.<br />
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Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
'''You can search by disease using:'''<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
'''You can search by human disease-associated gene using:'''<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
'''You can search by ''Drosophila melanogaster'' gene using:'''<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
'''The QuickSearch auto-completion feature is active in this tab; auto-completion works for''' <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Homologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. It can also be used to find paralogs within ''D. melanogaster'', as provided by DIOPT. The DIOPT dataset integrates ortholog/paralog predictions for humans and 9 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa. A related '''video tutorial''' can be found at [https://www.youtube.com/watch?v=JsNyrNG28M0 Using the Orthology search tool].<br />
<br />
To search for orthologs, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset).<br />
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To search for paralogs within ''D. melanogaster'', choose the DIOPT dataset and select ''D. melanogaster'' as '''both''' the input and output species.<br />
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Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''A. thaliana'' || [https://apps.araport.org/thalemine/keywordSearchResults.do?searchTerm= Araport] gene symbol (e.g. CDC2) or gene ID (e.g. AT3G48750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 824036)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog/paralog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given gene-pair relationship compared to the total number of tools that compute relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given gene has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given gene in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''Align''': link to an alignment between the given gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs/paralogs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''gene''': official gene symbol, as used in the relevant model organism database<br />
* '''gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given gene has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given gene in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any pairwise calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=170568FlyBase:QuickSearch2019-08-21T20:22:14Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Homologs tab| Homologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
<br />
All tabs search data for all species included in FlyBase. An option to filter by species is provided in the resulting hit-list.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://{{flybaseorg}}/vocabularies Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
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The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
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Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
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The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
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The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
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In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
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Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from all data classes of reports.<br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [[FlyBase:RNA-Seq Overview | RNA-Seq overview page]]. There are '''video tutorials''' available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern, or gene promoter expression pattern, as curated from the literature.<br />
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'''Search by curated expression pattern''' Click the option "'''by curated expression pattern'''". Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. Please note that you must fill either the '''Developmental Stage''' or '''Anatomy or Cell Type''' boxes to use this search option; you cannot fill only the '''Cellular Component''' box. Please note that you must use a valid controlled vocabulary term, and cannot search using a synonym. Synonyms will fail to autocomplete; you will instead see text reading "...no matching text suggestions...", and your query will produce no matches. You can use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to search with your synonym to find a valid Controlled Vocabulary term.<br />
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'''Search with qualifier terms ''' THIS FEATURE HAS BEEN TEMPORARILY DISABLED. You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled; you do, however, need to fill at least one <br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled, as only a small subset of expression pattern curation for driver or reporter alleles include a GO cellular component term, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=&id=GO:0043195 terminal bouton]. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''by curated expression pattern''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Expression terms''' column of the '''GAL4 etc''' hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Search by expression pattern of a particular gene''' Click the option "'''reflecting expression pattern of a particular gene'''". The form has one input box, '''Gene'''. You can enter either a valid FlyBase gene symbol, such as [http://{{flybaseorg}}/reports/FBgn0000490 dpp], or a valid FlyBase gene ID number, such as FBgn0000490; synonyms or full gene names will not work in this search. Please note that this search is only for drivers and/or reporters that have been curated as reflecting the expression pattern of a specific gene; this search will not find drivers/reporters with an expression pattern similar to that of the gene you have entered in the search box, nor will it find drivers/reporters that are associated with a specific gene, but have not been curated as reflecting expression of that gene. Please note: this search option is an alternative to the "'''by curated expression pattern'''" search option; you can choose only one of these two options.<br />
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IN PROGRESS'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for. Clicking through to the '''Allele Reports''', '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===Pathways tab===<br />
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This tab searches FlyBase-curated 'Pathway Reports' - sets of genes/gene products that have been experimentally shown to act within a pathway or to regulate a pathway.<br />
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To use, either start typing and select the appropriate Pathway Report name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Pathway Reports that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Pathway Reports to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Pathway Reports.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Note, as the GO is an ontology, all child terms will possess the property of the parent, therefore consider using '''Records annotated with this term OR any of its CHILDREN TERMS''' to get a complete gene list.<br />
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Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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'''You can search by disease using:'''<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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'''You can search by human disease-associated gene using:'''<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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'''You can search by ''Drosophila melanogaster'' gene using:'''<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
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'''The QuickSearch auto-completion feature is active in this tab; auto-completion works for''' <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Homologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. It can also be used to find paralogs within ''D. melanogaster'', as provided by DIOPT. The DIOPT dataset integrates ortholog/paralog predictions for humans and 9 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa. A related '''video tutorial''' can be found at [https://www.youtube.com/watch?v=JsNyrNG28M0 Using the Orthology search tool].<br />
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To search for orthologs, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset).<br />
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To search for paralogs within ''D. melanogaster'', choose the DIOPT dataset and select ''D. melanogaster'' as '''both''' the input and output species.<br />
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Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''A. thaliana'' || [https://apps.araport.org/thalemine/keywordSearchResults.do?searchTerm= Araport] gene symbol (e.g. CDC2) or gene ID (e.g. AT3G48750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 824036)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog/paralog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given gene-pair relationship compared to the total number of tools that compute relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given gene has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given gene in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''Align''': link to an alignment between the given gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs/paralogs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''gene''': official gene symbol, as used in the relevant model organism database<br />
* '''gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual prediction tools that support a given gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given gene has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given gene in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any pairwise calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=170311FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2019-04-04T14:44:53Z<p>Sian: /* Pamphlets and Handouts */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* ADRC 2019. FlyBase updates 2019. [[Media:FlyBase updates 2019.pdf|presentation]] (18 slides)<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* ADRC 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ADRC_2019_Pathways.pdf|pdf]]<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* EDRC 2017. Function-centered approaches for finding and analyzing genes within FlyBase. [[Media:EDRC_poster_function.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2019. New tools, features, and resources for 2019. [[Media:ADRC2019_NewTools.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:ADRC2019_NewTools.pdf&diff=170310File:ADRC2019 NewTools.pdf2019-04-04T14:40:47Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=170287FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2019-03-25T18:00:54Z<p>Sian: /* Posters */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:Disease_Navigation_poster_ADRC2019.pdf&diff=170286File:Disease Navigation poster ADRC2019.pdf2019-03-25T18:00:21Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=170285FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2019-03-25T17:45:41Z<p>Sian: </p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:GAL4_and_Tools_poster_ADRC2019.pdf&diff=170284File:GAL4 and Tools poster ADRC2019.pdf2019-03-25T17:43:52Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Downloads_Overview&diff=170217FlyBase:Downloads Overview2019-01-14T17:04:48Z<p>Sian: /* Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json.gz) */</p>
<hr />
<div>==Introduction==<br />
<br />
The "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page]" (referred to herein as the "Precomputed files" page) lists data files generated from the current release of FlyBase and links to the [ftp://ftp.flybase.net/releases/current/ current FTP repository]. Data from the previous five releases can be found on the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=archivedata3.html&title=Archived%20Releases Archived data files for recent releases]" page (referred to herein as the "Archived data" page), as well as links to servers hosting older releases of FlyBase, and all the release notes and news archives from FB2006_01. If you are looking for old data and cannot find it on the "Archived data" page please follow a link to the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
===Known issues===<br />
<br />
Safari does not connect properly to the FlyBase FTP site. You should be able to download individual files using Safari but you will not be able to browse the FTP repository.<br />
<br />
==The FTP archive==<br />
<br />
The "Main Data Set" section of the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Precomputed files]" page provides links to FlyBase FTP repository. The "Chado database" link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:<br />
<br />
$ psql -h chado.flybase.org -U flybase flybase<br />
<br />
The version running on this service is identical to the current web site release.<br />
<br />
The "Drosophila Data" section contains links to other sections of the FTP repository. The data can be accessed either by the version of FlyBase (The "[ftp://ftp.flybase.net/releases/current/ Current FTP repository]") or for sequence data by the annotation release of a particular Drosophila species (see the "[ftp://ftp.flybase.net/genomes/ Genomes FTP archive]")<br />
<br />
==General information about the available files==<br />
<br />
===File names===<br />
The first part of a filename always describes the content of the file, for example the file fbgn_annotation_ID_fb_2008_10.tsv.gz maps the primary FlyBase identifiers to the annotation symbols used for genes.<br />
<br />
Many of the precomputed data filenames also contain a release or version number. In the example above "fb_2008_10" denotes version FB2008_10 of FlyBase. Sequence data files, such as dmel-all-CDS-r5.13.fasta.gz, denote the annotation release that the data relates to as '-r5.13'. The 'r5' indicates the data is taken from the release 5 of the sequence assembly and the '13' after the decimal point specifies the annotation release.<br />
<br />
The following notation is used for different file formats: <br />
<br />
:'''Tab separated files''' are indicated by the extension ''''.tsv''''<br />
:'''[http://www.geneontology.org/GO.format.shtml#oboflat OBO format files]''', which are used for the ontologies, are denoted ''''.obo''''<br />
:'''Plain text''' files are given the extension ''''.txt''''<br />
:Files containing nucleic acid or polypeptide sequence data in the '''FASTA''' format are listed as ''''.fasta''''<br />
:'''GFF''' files include the suffix ''''.gff''''<br />
:'''GTF''' files include the suffix ''''.gtf''''<br />
:'''XML''' data files are denoted ''''.xml''''<br />
<br />
Most of the files listed on the "Precomputed files" page and the "Archived data" page are compressed with the [http://www.gzip.org/ GNU gzip] program. These files end with the suffix '.gz'. The ontology files are compressed in the ZIP file format, as indicated by the suffix '.zip'.<br />
<br />
===Accessing files===<br />
Files can be downloaded either directly through the web interface, or by using an ftp client such as wget to obtain the file from the FTP repository. Please note that at present Safari fails to connect to the FTP repository correctly, so we recommend that you use another browser if you wish to access the files through the web interface. The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file. Archived copies of the files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve this file for the FB2008_05 release, type:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
or more specifically:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_fb_2008_05.tsv.gz<br />
<br />
<br />
===Opening compressed files===<br />
Microsoft and Apple include built-in ZIP support in later versions of their operating systems. These files can also be opened with the free program [http://www.7-zip.org/ 7-zip].<br />
<br />
On OS X or Unix a GZIP compressed file can be extracted with the gunzip command. On a Windows machine we suggest that you use the program [http://www.7-zip.org/ 7-zip] to open these files, because several people have reported problems using WinZip. You should be able to open and read the resulting file with any text editor. <br />
<br />
<br />
==Types of files available==<br />
<br />
===XML files===<br />
<br />
These files are generated from the PostgreSQL Chado database for each release of FlyBase. The Chado XML files contain all the information used to generate the report pages and reflect the organization of the data in the database. The DTDs for these XML files, listing the structure of the files, are posted in the chado-xml directory of the FTP repository for each release. For the latest versions of the DTDs please see:<br />
<br />
ftp://ftp.flybase.net/releases/current/chado-xml/<br />
<br />
The XML files can also be obtained directly from the "Precomputed files" page by clicking on the "download" link under the ChadoXML heading in the appropriate section. The Chado XML files are available for genes, alleles, stocks, transcripts, polypeptides, insertions, transgenic (recombinant) constructs, aberrations, balancers, clones, and references.<br />
<br />
===Ontology files===<br />
<br />
The [http://{{flybaseorg}}/static_pages/docs/refman/refman-G.html#G.2. controlled vocabularies] (aka ontologies) used by FlyBase are available under the Ontology Terms section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page. Each controlled vocabulary is described in detail in [[FlyBase:Controlled vocabularies used by FlyBase|section G.2]]. of the Reference Manual. The files are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and are designed to be used with the free [http://www.oboedit.org/ OBO-Edit] tool.<br />
<br />
Controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects. On the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page the frozen versions of the controlled vocabularies used for the current release of FlyBase are available, and there are also links to the current 'live' versions maintained by the [http://www.obofoundry.org/ Open Biomedical Ontology] group.<br />
<br />
Frozen versions of the controlled vocabularies used for previous releases of FlyBase are available on the "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" page, and in the following directories of the FTP repository:<br />
<br />
ftp://ftp.flybase.net/releases/<RELEASE_NUMBER>/precomputed_files/ontologies/<br />
<br />
For example see:<br />
<br />
ftp://ftp.flybase.net/releases/FB2008_03/precomputed_files/ontologies/<br />
<br />
===FASTA files===<br />
<br />
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:<br />
<br />
'''dmel-all-<data type>-r<release-number>.fasta.gz'''<br />
<br />
or<br />
<br />
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''<br />
<br />
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome. <br />
<br />
{| class= "wikitable"<br />
!Data Type <br />
!Content Description<br />
|-<br />
|'''aligned ''' <br />
|The region of genomic sequence that analysis features align to.<br />
|-<br />
|'''CDS''' <br />
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.<br />
|-<br />
|'''chromosome'''<br />
|The sequence of each chromosome arm.<br />
|-<br />
|'''clones''' <br />
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.<br />
|-<br />
|'''exon ''' <br />
|The sequence of each exon split up into individual FASTA records.<br />
|-<br />
|'''five_prime_UTR'''<br />
|The sequence of 5' untranslated regions.<br />
|-<br />
|'''gene''' <br />
|The sequence of the gene span.<br />
|-<br />
|'''gene_extended2000''' <br />
|The sequence of the gene span with 2000 base pairs added upstream and downstream.<br />
|-<br />
|'''intergenic'''<br />
|The sequence of chromosomal regions between genes that do not contain known gene models.<br />
|-<br />
|'''intron''' <br />
|The sequence of each intron split up into individual FASTA records.<br />
|-<br />
|'''miRNA''' <br />
|The sequence of transcripts that are typed as micro RNAs.<br />
|-<br />
|'''miscRNA''' <br />
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.<br />
|-<br />
|'''ncRNA''' <br />
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).<br />
|-<br />
|'''predicted''' <br />
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.<br />
|-<br />
|'''pseudogene''' <br />
|The sequence of transcripts that are typed as pseudogenes.<br />
|-<br />
|'''sequence_features''' <br />
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.<br />
|-<br />
|'''synteny'''<br />
|The sequence of syntenic regions between two species.<br />
|-<br />
|'''three_prime_UTR'''<br />
|The sequence of 3' untranslated regions.<br />
|-<br />
|'''transcript'''<br />
|The sequence of transcripts that are typed as messenger RNAs (mRNA).<br />
|-<br />
|'''translation''' <br />
|The resulting protein sequence from protein coding transcripts.<br />
|-<br />
|'''transposon'''<br />
|The sequence of transposable elements.<br />
|-<br />
|'''tRNA''' <br />
|The sequence of transcripts that are typed as transfer RNAs (tRNA).<br />
|}<br />
<br />
<br />
====FASTA header format====<br />
<br />
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format<br />
<br />
'''field_name=value;'''<br />
<br />
Multiple field values are separated by commas<br />
<br />
'''field_name=value1,value2;'''<br />
<br />
This table describes some of the field names found in our FASTA headers <br />
<br />
{|class = "wikitable"<br />
<br />
!Field Name<br />
!Description<br />
|-<br />
|'''type''' <br />
|The feature type of the FASTA sequence record.<br />
|-<br />
|'''loc''' <br />
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.<br />
|-<br />
|'''ID''' <br />
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.<br />
|-<br />
|'''name'''<br />
|The name or symbol of the feature.<br />
|-<br />
|'''dbxref'''<br />
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.<br />
|-<br />
|'''MD5'''<br />
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.<br />
|-<br />
|'''length'''<br />
|The length of the sequence found in the FASTA record.<br />
|-<br />
|'''release'''<br />
|The release number denotes the annotation release which this FASTA record corresponds to.<br />
|-<br />
|'''species'''<br />
|The species abbreviation that this FASTA record corresponds to.<br />
|}<br />
<br />
<br />
===GFF files===<br />
<br />
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features. The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gff/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gff/<br />
<br />
For melanogaster, there are 3 GFF files distributed, they include:<br />
<br />
:'''dmel-all-r<release-number>.gff.gz'''<br />
::Contains all chromosome arms<br />
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''<br />
::Same as above except all match and match_part features have been removed<br />
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''<br />
::Contains only a single chromosome arm as identifed by the filename<br />
<br />
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues. <br />
<br />
===GTF files===<br />
<br />
The FlyBase GTF files follow the [http://mblab.wustl.edu/GTF22.html GTF v2.2] specification. The GTF files contain feature line definitions for gene models. The GTF are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gtf/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gtf/<br />
<br />
===Precomputed data text files===<br />
<br />
Precomputed data files that contain useful sets of data are generated for every release of FlyBase. For example, the file fbgn_NAseq_Uniprot_fb_2008_10.tsv.gz contains the mapping between valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] and the corresponding nucleic acid and protein accession numbers used by DDBJ/EMBL/GenBank and UniprotKB/Swiss-Prot/TrEMBL. These files can be found under the "Other" heading of each section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" and "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" pages, and are also available under the precomputed_files directory of each FlyBase release in the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.<br />
<br />
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.<br />
<br />
Each precomputed data file available for download on the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page contains the complete data set for the FlyBase release. Please note, if you are only looking for information on a defined subset of genes, or other FlyBase data type, you can query the current set of precomputed data files through the [http://{{flybaseorg}}/batchdownload Batch Download] tool to obtain the data you require. This approach is described in more detail in [https://wiki.flybase.org/wiki/FlyBase:Batch_Download this] help document.<br />
<br />
==Contents of the precomputed data text files listed by section==<br />
<br />
===Main data set===<br />
<br />
====Postgres Chado database dump====<br />
=====Chado database (ftp://ftp.flybase.net/releases/current/psql)=====<br />
The entire SQL Chado database is available for download. Follow the "README" directions herein.<br />
<br />
====Drosophila data====<br />
=====Current FTP repository (ftp://ftp.flybase.net/releases/current/)=====<br />
All files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Current Chado-XML repository (ftp://ftp.flybase.net/releases/current/chado-xml)=====<br />
All Chado XML files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Genomes FTP archive (ftp://ftp.flybase.net/genomes/)=====<br />
All FlyBase genome and genome annotation files are available for various Drosophila species. Formats include Chado XML, DNA, FASTA, GFF and GTF. Files from both the current release and previous FlyBase releases are offered. For release FB2018_05 and earlier, data is available for each of the original 12 sequenced Drosophila species. From release FB2018_06 onward, data is available only for D. melanogaster, D. simulans, D. ananassae, D. pseudoobscura and D. virilis.<br />
<br />
===Synonyms===<br />
<br />
====FlyBase Synonyms (fb_synonym_*.tsv)====<br />
The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).<br />
<br />
The file includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
* genes from drosophilid species and genes from non-drosophilids that have been introduced into transgenic flies<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''primary_FBid''' <br />
|Primary FlyBase identifier for the object.<br />
|-<br />
|'''organism_abbreviation''' <br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin.<br />
|-<br />
|'''current_symbol'''<br />
|Current symbol used in FlyBase for the object.<br />
|-<br />
|'''current_fullname''' <br />
|Current full name used in FlyBase for the object.<br />
|-<br />
|'''fullname_synonym(s)''' <br />
|Non-current full name(s) associated with the object (comma separated values).<br />
|-<br />
|'''symbol_synonym(s)'''<br />
|Non-current symbol(s) associated with the object (comma separated values).<br />
|-<br />
|}<br />
<br />
===Genes===<br />
<br />
====Genes data (Chado XML)====<br />
<br />
====Genetic interaction table (gene_genetic_interactions_*.tsv)====<br />
The file reports the summary of gene-level genetic interactions in FlyBase. This data is computed from the allele-level genetic interaction data captured by FlyBase curators.<br />
<br />
The file includes information for Dmel genes only.<br />
<br />
Interactions involving any of the following kinds of allele are considered when the gene-level genetic interaction data is computed:<br />
<br />
* classical mutations<br />
* alleles carried on transgenic constructs<br />
* loss-of-function mutations<br />
* gain-of-function mutations<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Starting_gene(s)_symbol''' <br />
|Current FlyBase symbol of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Starting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Interacting_gene(s)_symbol'''<br />
|Current FlyBase symbol of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interacting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interaction_type''' <br />
|Type of interaction observed, either 'suppressible' or 'enhanceable'.<br />
|-<br />
|'''Publication_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if the same genetic interaction has been reported in multiple references, multiple rows will exist for that genetic interaction in the file.<br />
<br />
* 'suppressible' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are suppressed by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
* 'enhanceable' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are enhanced by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
''e.g.''<br />
<br />
Pten&emsp;FBgn0026379&emsp;Akt1&emsp;FBgn0010379&emsp;suppressible&emsp;FBrf0127089<br />
<br />
indicates that phenotype(s) caused by a mutation of Pten are suppressed by a mutation of Akt1.<br />
<br />
* For cases where multiple genes are simultaneously mutated in either (or both) the starting and interacting genotype, then the genes involved are separated by a '|' in the relevant columns. In this case, the order of the list of symbols and of the list of ids in columns 1 and 2, or in columns 3 and 4 respectively are the same, so that the FBgn corresponding to the symbol for each gene can easily be identified.<br />
<br />
''e.g.''<br />
<br />
robo1|sli&emsp;FBgn0005631|FBgn0264089&emsp;RhoGAP93B&emsp;FBgn0038853&emsp;enhanceable&emsp;FBrf0191476<br />
<br />
indicates that:<br />
* phenotype(s) caused by a robo1, sli double mutant combination are enhanced by a mutation of RhoGAP93B.<br />
* FBgn0005631 corresponds to robo1, FBgn0264089 corresponds to sli<br />
<br />
<br />
<br />
====RNA-Seq RPKM values (gene_rpkm_report_fb_*.tsv.gz)====<br />
This file reports gene expression values based on RNA-Seq experiments, calculated as reads per kilobase per million reads (RPKM). RPKM values are calculated only for the unique exonic regions of the gene (excluding segments that overlap other genes), except for genes derived from dicistronic/polycistronic transcripts, in which case all exon regions are used in the RPKM expression calculation.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Release_ID'''<br />
|The D. melanogaster annotation set version from which the gene model used in the analysis derives.<br />
|-<br />
|'''FBgn#'''<br />
|The unique FlyBase gene ID for this gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|The official FlyBase symbol for this gene.<br />
|-<br />
|'''Parent_library_FBlc#'''<br />
|The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''Parent_library_name'''<br />
|The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''RNASource_FBlc#'''<br />
|The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RNASource_name'''<br />
|The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RPKM_value'''<br />
|The RPKM expression value for the gene in the specified RNA-Seq experiment.<br />
|-<br />
|'''Bin_value'''<br />
|The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression).<br />
|-<br />
|'''Unique_exon_base_count'''<br />
|The number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts.<br />
|-<br />
|'''Total_exon_base_count'''<br />
|The number of bases in all exons of this gene.<br />
|-<br />
|'''Count_used'''<br />
|Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Physical interaction table (physical_interactions_fb_*.tsv.gz)====<br />
This file reports unique gene pairs with curated support for some type of physical interaction. The file does not currently distinguish between genes that are involved in protein-protein or RNA-protein interactions (or both).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_FBgn1'''<br />
|The unique FlyBase gene ID for the first gene of the interacting pair.<br />
|-<br />
|'''gene_symbol1'''<br />
|The official FlyBase symbol for the first gene of the interacting pair.<br />
|-<br />
|'''gene_FBgn2'''<br />
|The unique FlyBase gene ID for the second gene of the interacting pair.<br />
|-<br />
|'''gene_symbol2'''<br />
|The official FlyBase symbol for the second gene of the interacting pair.<br />
|-<br />
|'''FBrf(s)'''<br />
|The unique FlyBase IDs for the publications supporting this interaction.<br />
|-<br />
|'''FBig_id'''<br />
|The unique FlyBase ID for this pairwise interaction.<br />
|-<br />
|'''#_reported_interactions'''<br />
|The number of distinct experiments in support of this interaction.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction MITAB file (physical_interactions_mitab_fb_*.tsv.gz)====<br />
This file reports each individual experiment curated by FlyBase that supports a physical interaction between two gene products. There can be multiple experiments (multiple rows in the file) between products of the same gene pair. Interaction molecule types currently curated are protein-protein, protein-RNA or RNA-RNA. <br />
<br />
This file is in PSI-MI TAB format, a tab-delimited format developed by the HUPO Proteomics Standards Initiative (PSI) Molecular Interactions (MI) working group to facilitate interactomics data comparison and exchange. Details on the general MITAB format can be found [https://psicquic.github.io/MITAB27Format.html here]. The file makes use of the Molecular Interactions ontology which can be searched or browsed [https://www.ebi.ac.uk/ols/ontologies/mi here]. Fields are filled with “-” if values are missing or not relevant.<br />
<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading<br />
!General format <br />
!FlyBase example<br />
!Content description<br />
|-<br />
|'''1'''<br />
|'''ID(s) Interactor A'''<br />
|database:identifier<br />
|flybase:FBgn0002121<br />
|The unique Flybase identifier for the first gene of the interacting pair.<br />
|-<br />
|'''2'''<br />
|'''ID(s) Interactor B'''<br />
|”<br />
|”<br />
|The unique Flybase identifier for the second gene of the interacting pair.<br />
|-<br />
|'''3'''<br />
|'''Alt ID(s) Interactor A'''<br />
|database:identifier<br />
|<nowiki>flybase:CG2671|entrez gene/locuslink:33156</nowiki><br />
|<nowiki>The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|”.</nowiki><br />
|-<br />
|'''4'''<br />
|'''Alt ID(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''5'''<br />
|'''Alias(es) Interactor A'''<br />
|database:name(alias type)<br />
|flybase:l(2)gl(gene name)<br />
|The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.<br />
|-<br />
|'''6'''<br />
|'''Alias(es) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''7'''<br />
|'''Interaction Detection Method(s)'''<br />
|ontology:identifier(method name)<br />
|psi-mi:"MI:0006"(anti bait coimmunoprecipitation)<br />
|The assay used to detect the interaction, taken from the psi-mi ontology.<br />
|-<br />
|'''8'''<br />
|'''Publication 1st Author(s)'''<br />
|surname initial(s) (publication year)<br />
|Betschinger K. (2003)<br />
|The first author and year of the publication where the interaction is described.<br />
|-<br />
|'''9'''<br />
|'''Publication ID(s)'''<br />
|database:identifier<br />
|<nowiki>flybase:FBrf0157155|pubmed:12629552</nowiki><br />
|<nowiki>The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.</nowiki><br />
|-<br />
|'''10'''<br />
|'''Taxid Interactor A'''<br />
|taxid:identifier<br />
|taxid:7227("Drosophila melanogaster")<br />
|The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.<br />
|-<br />
|'''11'''<br />
|'''Taxid Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''12'''<br />
|'''Interaction Type(s)'''<br />
|ontology:identifier(interaction type)<br />
|psi-mi:"MI:0915"(physical association)<br />
|Taken from the psi-mi ontology. Most often “physical association” for FlyBase.<br />
|-<br />
|'''13'''<br />
|'''Source Database(s)'''<br />
|ontology:identifier(database name)<br />
|psi-mi:"MI:0478"(flybase)<br />
|All interactions are curated by FlyBase.<br />
|-<br />
|'''14'''<br />
|'''Interaction Identifier(s)'''<br />
|database:identifier<br />
|flybase:FBrf0157155-13.coIP.WB<br />
|The unique FlyBase identifier for this interaction.<br />
|-<br />
|'''15'''<br />
|'''Confidence Value(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''16'''<br />
|'''Expansion Method(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''17'''<br />
|'''Biological Role(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''18'''<br />
|'''Biological Role(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''19'''<br />
|'''Experimental Role(s) Interactor A'''<br />
|ontology:identifier(experimental role name)<br />
|psi-mi:"MI:0496"(bait)<br />
|The role played by the interactor in the experiment. Taken from the psi-mi ontology.<br />
|-<br />
|'''20'''<br />
|'''Experimental Role(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''21'''<br />
|'''Type(s) Interactor A'''<br />
|ontology:identifier(interactor type name)<br />
|psi-mi:"MI:0326"(protein)<br />
|The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.<br />
|-<br />
|'''22'''<br />
|'''Type(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''23'''<br />
|'''Xref(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''24'''<br />
|'''Xref(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''25'''<br />
|'''Interaction Xref(s)'''<br />
|database:identifier<br />
|flybase:FBig0000000103<br />
|<nowiki>Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.</nowiki><br />
|-<br />
|'''26'''<br />
|'''Annotation(s) Interactor A'''<br />
|topic:text<br />
|isoform-comment:a isoform<br />
|Information on whether the interaction is specific to a particular interactor isoform.<br />
|-<br />
|'''27'''<br />
|'''Annotation(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''28'''<br />
|'''Interaction Annotation(s)'''<br />
|topic:text<br />
|molecular source:Source was cell extract of S2 cell line; bait produced from endogenous gene; prey produced from endogenous gene.|comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.<br />
|Describes the source(s) of the interaction participants and includes free text comments about the interaction.<br />
|-<br />
|'''29'''<br />
|'''Host Organism(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''30'''<br />
|'''Interaction Parameters'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''31'''<br />
|'''Creation Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''32'''<br />
|'''Update Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''33'''<br />
|'''Checksum Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''34'''<br />
|'''Checksum Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''35'''<br />
|'''Interaction Checksum'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''36'''<br />
|'''Negative'''<br />
|<br />
|FALSE<br />
|All interactions in FlyBase are positive.<br />
|-<br />
|'''37'''<br />
|'''Feature(s) Interactor A'''<br />
|feature_type:range(text)<br />
|sufficient binding region:aa 1-58(N-terminal region)<br />
|Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.<br />
|-<br />
|'''38'''<br />
|'''Feature(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''39'''<br />
|'''Stoichiometry Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''40'''<br />
|'''Stoichiometry Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''41'''<br />
|'''Identification Method(s) Participant A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''42'''<br />
|'''Identification Method(s) Participant B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|}<br />
<br />
<br />
====Functional complementation table (gene_functional_complementation_*.tsv)====<br />
<br />
This file reports when functional complementation of Dmel genes by non-Dmel orthologs has been observed. This data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature. The file contains a list of gene Dmel - to - non-Dmel-ortholog gene pairs where a transgenic construct/mutant allele of the non-Dmel ortholog has been shown to at least partially suppress mutant phenotype(s) of an allele of the Dmel gene.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''Dmel gene (symbol)'''<br />
|Current FlyBase symbol of Dmel gene.<br />
|-<br />
|'''2'''<br />
|'''Dmel gene (FBgn)'''<br />
|Current FlyBase identifier (FBgn#) of Dmel gene in column 1.<br />
|-<br />
|'''3'''<br />
|'''Functionally complementing ortholog (symbol)'''<br />
|Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''4'''<br />
|'''Functionally complementing ortholog (FBgn#)'''<br />
|Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''5'''<br />
|'''Supporting_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if multiple references support the same functional complementation statement, multiple rows will exist for that statement in the file.<br />
<br />
<br />
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====<br />
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, UniProtKB/SwissProt/TrEMBL protein accessions, NCBI Entrez gene IDs and NCBI RefSeq transcript and protein accessions associated with FlyBase genes.<br />
<br />
The file includes:<br />
* nuclear genes with sequence accession numbers<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes without sequence accession numbers<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''2'''<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''3'''<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''4'''<br />
|'''nucleotide_accession'''<br />
|EMBL/GenBank/DDBJ nucleotide accession associated with the gene.<br />
|-<br />
|'''5'''<br />
|'''na_based_protein_accession'''<br />
|EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column<br />
|-<br />
|'''6'''<br />
|'''UniprotKB/Swiss-Prot/TrEMBL_accession'''<br />
|UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.<br />
|-<br />
|'''7'''<br />
|'''EntrezGene_ID'''<br />
|NCBI Entrez ID associated with the gene.<br />
|-<br />
|'''8'''<br />
|'''RefSeq_transcripts'''<br />
|NCBI RefSeq transcript accession associated with the gene.<br />
|-<br />
|'''9'''<br />
|'''RefSeq_proteins'''<br />
|NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.<br />
<br />
* A single row contains '''only''' information about an EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession '''or''' an NCBI Entrez gene ID '''or''' an NCBI RefSeq transcript accession.<br />
<br />
* For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 4 ('nucleotide_accession'). If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 4, this protein accession is listed in column 5 ('na_based_protein_accession'). In this case, columns 6, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 6 ('UniprotKB/Swiss-Prot/TrEMBL_accession'). In this case, columns 4, 5, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI Entrez gene, an ID associated with the gene is listed in column 7 ('EntrezGene_ID'). In this case, columns 4, 5, 6, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI RefSeq accession, a transcript accession associated with the gene is listed in column 8 ('RefSeq_transcripts'). If there is also an NCBI RefSeq protein accession associated with that gene '''and''' with the transcript accession in column 8, this protein accession is listed in column 9 ('RefSeq_proteins'). In this case, columns 4, 5, 6 and 7 are always empty.<br />
<br />
<br />
<br />
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====<br />
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''secondary_FBgn#(s)'''<br />
|Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).<br />
|-<br />
|'''annotation_ID'''<br />
|Current annotation identifier associated with the gene.<br />
|-<br />
|'''secondary_annotation_ID(s)'''<br />
|Secondary annotation identifier(s) associated with the gene (comma separated values).<br />
|-<br />
|}<br />
Notes:<br />
<br />
* If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702). <br />
<br />
<br />
<br />
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====<br />
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.<br />
<br />
The file includes:<br />
* non-melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* ''D. melanogaster'' genes<br />
* non-melanogaster genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''gene_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GLEANR_ID'''<br />
|GLEANR identifier assigned by the AAA Consortium.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====<br />
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.<br />
<br />
The file includes:<br />
* genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FlyBase_FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FlyBase_FBtr'''<br />
|Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.<br />
|-<br />
|'''FlyBase_FBpp'''<br />
|Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript and the polypeptide it encodes (if relevant). Thus if a gene encodes multiple isoforms, multiple rows with exist for that gene in the file.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====<br />
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.<br />
<br />
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.<br />
<br />
The file includes the following '''Dmel''' genes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
Notes:<br />
<br />
* Each line of the file '''can contain many''' tab separated columns:<br />
<br />
* '''The first column of a line''' contains the valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] of a gene.<br />
* '''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====<br />
The file is generated from the location of Affy2 oligos exactly as [[FlyBase:FilesOverview#5.2.6|described for Affy1 oligos]] above.<br />
<br />
<br />
<br />
====Genes GO data (gene_association.fb)====<br />
The file contains the [http://www.geneontology.org/ Gene Ontology] (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.<br />
<br />
The file includes the following Dmel genes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
The columns of the file are described in [[FlyBase:Gene Ontology (GO) Annotation|section G.3.1.]] of the Reference manual.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_*.tsv)====<br />
The file reports available localization information for FlyBase genes.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''current_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBid'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''recombination_loc'''<br />
|recombination map location.<br />
|-<br />
|'''cytogenetic_loc'''<br />
|cytogenetic location.<br />
|-<br />
|'''sequence_loc'''<br />
|genomic location.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Automated gene summaries (automated_gene_summaries.tsv)====<br />
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|FlyBase ID. The Valid FlyBase identifier number for the gene.<br />
|-<br />
|'''-'''<br />
|The gene summary as a string of plain text.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Gene Snapshots (gene_snapshots_*.tsv)====<br />
The file contains in plain text the gene snapshot information visible on gene report pages.<br />
<br />
It includes only Dmel protein coding genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier number for the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase symbol of the gene.<br />
|-<br />
|'''GeneName'''<br />
|Current FlyBase name of the gene.<br />
|-<br />
|'''datestamp'''<br />
|Date on which the information was last reviewed.<br />
|-<br />
|'''gene_snapshot_text'''<br />
|Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Unique protein isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their unique protein isoforms.<br />
<br />
The file includes:<br />
* melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* melanogaster genes not located to the sequence<br />
* non-melanogaster genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FB_gene_symbol'''<br />
|Current FlyBase gene symbol of the gene.<br />
|-<br />
|'''representative_protein'''<br />
|Current FlyBase protein symbol of the representative protein isoform.<br />
|-<br />
|'''identical_protein(s)'''<br />
|Current FlyBase protein symbol(s) of identical protein isoforms.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNA genes (TSV) (ncRNA_genes_fb_*.tsv.gz)====<br />
This file reports all genes encoding ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in TSV format. Pseudogenes are excluded.<br />
<br />
Columns are:<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''accession_id'''<br />
|INSDC accession ID.<br />
|-<br />
|'''FB_gene_ID'''<br />
|Current FlyBase gene identifier (FBgn#).<br />
|-<br />
|'''species_FB_annotation_ID(locus_tag)'''<br />
|Current FlyBase annotation ID, in the form "<species abbreviation>_<annotation_ID>", which equates to the 'locus tag' field in INSDC records.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Gene groups===<br />
====Gene group data (gene_group_data_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with their hierarchical relationships (where relevant) and member genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''Parent_FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Parent_FB_group_symbol'''<br />
|Current FlyBase symbol of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Group_member_FB_gene_id'''<br />
|Current FlyBase identifier (FBgn##) of member gene (if terminal group).<br />
|-<br />
|'''Group_member_FB_gene_symbol'''<br />
|Current FlyBase symbol of member gene (if terminal group).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Where groups are arranged into hierarchies:<br />
** the member genes are only associated with the terminal subgroups,<br />
** the immediate parent of any subgroup is identified in the ‘Parent_FB_group_id' and 'Parent_FB_group_symbol' columns.<br />
<br />
* Separate lines are used for each member gene, meaning that each terminal group is listed multiple times (equal to the number of member genes).<br />
<br />
<br />
<br />
====Gene groups with HGNC IDs (gene_groups_HGNC_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with the corresponding HGNC 'gene family' ID (where relevant).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''HGNC_family_ID'''<br />
|HGNC ID of equivalent human 'gene family'.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* The absence of an HGNC_family_ID entry indicates there is no equivalent HGNC gene family for that FlyBase gene group.<br />
<br />
* Because of different sub-group structures (etc), a single HGNC family may be associated with multiple FlyBase gene groups.<br />
<br />
* Similarly, a single FlyBase gene group may be associated with multiple HGNC gene families - these are shown on separate lines.<br />
<br />
<br />
<br />
===Alleles and Stocks===<br />
====Allele data (Chado XML)====<br />
<br />
====Stock data (Chado XML)====<br />
<br />
====Stock data (stocks_*.tsv.gz)====<br />
This file reports genetic components and related information about Stocks in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
!Example<br />
|-<br />
|'''FBst'''<br />
|The unique identifier assigned to this stock by FlyBase.<br />
|FBst0000002<br />
|-<br />
|'''collection_short_name'''<br />
|A short name for the stock collection that holds the stock.<br />
|Bloomington<br />
|-<br />
|'''stock_type_cv'''<br />
|The controlled vocabulary term and unique identifier that describe the state of the stock.<br />
|living stock ; FBsv:0000002<br />
|-<br />
|'''species'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of the stock.<br />
|Dmel<br />
|-<br />
|'''FB_genotype'''<br />
|Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.<br />
|w[*]; betaTub60D[2] Kr[If-1]/CyO<br />
|-<br />
|'''description'''<br />
|Genetic components of the stock as provided to FlyBase by the collection that holds the stock.<br />
|FlyTrap: ZCL1796 III<br />
|-<br />
|'''stock_number'''<br />
|The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.<br />
|110818<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genetic interactions (allele_genetic_interactions_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''interaction'''<br />
|Interaction information associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single interaction from a single reference. Thus if multiple genetic interactions have been reported for a given allele, or if multiple references report the same interaction for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Phenotypic data (allele_phenotypic_data_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''phenotype'''<br />
|Phenotypic data associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes: <br />
<br />
* Each row contains information about a single phenotype from a single reference. Thus if multiple phenotypes have been reported for a given allele, or if multiple references report the same phenotype for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Alleles <=> Genes (fbal_to_fbgn_fb_*.tsv)====<br />
This file reports the relationship between gene identifiers and the identifiers used for alleles of these genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''AlleleID'''<br />
|Current FlyBase identifier (FBal#) of the allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current symbol of the allele.<br />
|-<br />
|'''GeneID'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Orthologs===<br />
<br />
====Drosophila Orthologs (dmel_orthologs_in_drosophila_species_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their orthologs in other sequenced Drosophila genomes, as determined by OrthoDB. (The version of OrthoDB currently being used is shown in the 'Orthologs' -> 'Orthologs (via OrthoDB)' section of a Gene Report.)<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Ortholog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_Arm/Scaffold'''<br />
|Arm upon which the non-melanogaster orthologous gene is localized.<br />
|-<br />
|'''Ortholog_Location'''<br />
|Location of non-melanogaster orthologous gene on the arm.<br />
|-<br />
|'''Ortholog_Strand'''<br />
|Strand of non-melanogaster orthologous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''OrthoDB_Group_ID'''<br />
|OrthoDB orthology group ID to which the pair-wise association belongs.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association beween a ''D. melanogaster'' gene and a non-melanogaster ortholog. Thus, multiple rows exist for each ''D. melanogaster'' gene in the file.<br />
<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dmel_gene_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Dmel_gene_symbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Human_gene_HGNC_ID'''<br />
|HGNC ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_OMIM_ID'''<br />
|OMIM ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_symbol'''<br />
|HGNC gene symbol of orthologous human gene.<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|'''OMIM_Phenotype_IDs'''<br />
|OMIM Phenotype ID of orthologous human gene (comma separated values).<br />
|-<br />
|'''OMIM_Phenotype_IDs[name]'''<br />
|OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets). Multiple phenotype[name] entries are separated by a comma.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Human disease===<br />
<br />
====Human disease model data (allele_human_disease_model_data_fb_*.tsv.gz)====<br />
This file reports all experimental-based disease model annotations, associated with alleles, that have been curated for ''D. melanogaster''. 'Alleles' encompasses both classical alleles and transgenic alleles; the latter may relate to transgenic constructs of ''D. melanogaster'' genes or non-''D. melanogaster'' genes, often human genes. These are the data reported in the "Human Disease Model Data" -> "Disease Ontology" section of the Allele Report, which are repeated in the "Human Disease Model Data" -> "Alleles Reported to Model Human Disease (Disease Ontology)" section of the Gene Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBal_ID'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current FlyBase symbol of allele.<br />
|-<br />
|'''DOID_qualifier'''<br />
|Annotation qualifier - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.<br />
|-<br />
|'''DOID_term'''<br />
|Disease Ontology term.<br />
|-<br />
|'''DOID_ID'''<br />
|Disease Ontology ID.<br />
|-<br />
|'''Evidence/interacting_alleles'''<br />
|Evidence code, with interacting allele(s) where appropriate. Evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma.<br />
|-<br />
|'''Reference_FBid'''<br />
|Current FlyBase identifier (FBrf#) of the publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
This is identical to the file of the same name listed under the 'Orthologs' section above. <br />
<br />
<br />
<br />
===Nomenclature===<br />
<br />
====Species abbreviation list (species-ab.gz)====<br />
<br />
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.<br />
<br />
There are 8 columns of data in the file, each separated by " | ".<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Internal_id'''<br />
|The Primary [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the organism.<br />
|-<br />
|'''Taxgroup'''<br />
|A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".<br />
|-<br />
|'''Abbreviation'''<br />
|The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.<br />
|-<br />
|'''Genus'''<br />
|The genus name of the organism.<br />
|-<br />
|'''Species name'''<br />
|The species name of the organism.<br />
|-<br />
|'''Common name'''<br />
|The common name of the organism. This column may be blank.<br />
|-<br />
|'''Comment'''<br />
|A free text field for additional comments. This column may be blank.<br />
|-<br />
|'''Ncbi-taxon-id'''<br />
|The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.<br />
|-<br />
|}<br />
<br />
An html version of this file is also available - see the [[FlyBase:Abbreviations|Species Abbreviations]] page.<br />
<br />
<br />
<br />
===Ontology Terms===<br />
====Frozen files used for this release of FlyBase====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
* FBdv: fly_development<br />
* FBcv: flybase controlled vocabulary<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
====Current 'Live' Files====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_anatomy.obo' version''<br />
* FBdv: fly_development<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_development.obo' version''<br />
* FBcv: flybase controlled vocabulary<br />
''Note: link points to the ontology version fbcv-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'flybase_controlled_vocabulary.obo' version''<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
===Genomes: Annotation and Sequence===<br />
====All Sequenced Drosophila Species====<br />
<br />
Links are available to the following FTP repositories:<br />
<br />
* Current FTP repository<br />
* Current FastA repository<br />
* Current GFF repository<br />
<br />
* FTP archive (previous releases)<br />
<br />
* Current list of individual FASTA files<br />
* Current list of individual GFF files<br />
<br />
For release FB2018_06 onward, the above links are available for the following sequenced Drosophila species:<br />
<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila melanogaster<br />
|Dmel<br />
|-<br />
|Drosophila ananassae<br />
|Dana<br />
|-<br />
|Drosophila pseudoobscura pseudoobscura<br />
|Dpse<br />
|-<br />
|Drosophila simulans<br />
|Dsim<br />
|-<br />
|Drosophila virilis<br />
|Dvir<br />
|-<br />
|}<br />
<br />
<br />
For earlier archived releases, the above links are also available for these additional species (other members of the original 12 sequenced Drosophila species):<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila erecta<br />
|Dere<br />
|-<br />
|Drosophila grimshawi<br />
|Dgri<br />
|-<br />
|Drosophila mojavensis<br />
|Dmoj<br />
|-<br />
|Drosophila persimilis<br />
|Dper<br />
|-<br />
|Drosophila sechellia<br />
|Dsec<br />
|-<br />
|Drosophila willistoni<br />
|Dwil<br />
|-<br />
|Drosophila yakuba<br />
|Dyak<br />
|-<br />
|}<br />
<br />
===Transcripts and Polypeptides===<br />
<br />
====Transcript data (Chado XML)====<br />
<br />
====Polypeptide data (Chado XML)====<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Transposons, Transgenic Constructs, and Insertions===<br />
<br />
====Insertions (Chado XML)====<br />
====Transgenic Constructs (Chado XML)====<br />
<br />
<br />
====Transgenic construct maps (construct_maps.zip)====<br />
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the respective recombinant construct or transgenic transposon.<br />
<br />
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.<br />
<br />
====Map data for insertions (insertion_mapping_*.tsv)====<br />
The insertion mapping table reports available localization information for '''Dmel''' insertions.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''insertion_symbol'''<br />
|Current symbol of insertion.<br />
|-<br />
|'''FBti#'''<br />
|Current FlyBase identifier (FBti#) of insertion<br />
.<br />
|-<br />
|'''genomic_location'''<br />
|Genomic location of insertion.<br />
|-<br />
|'''range'''<br />
|Range (t/f) indicates whether genomic location is range or single base.<br />
|-<br />
|'''orientation'''<br />
|Orientation (1/0) indicates orientation of insertion on chromosome.<br />
|-<br />
|'''estimated_cytogenetic_location'''<br />
|Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.<br />
|-<br />
|'''observed_cytogenetic_location'''<br />
|Observed cytogenetic location reported in the literature.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====<br />
This is a file of 'canonical' sequences of the transposable elements from Drosophila maintained by M. Ashburner.<br />
<br />
The first section of the file outlines the history and revisions to the file and also lists the current set of elements, their size and whether the subsequent sequence data is complete.<br />
<br />
The second section of the file, which is separated from the first by a line of "_" characters contains the sequence data of all the elements in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL format]. The record for each element starts with a line prefixed by "ID" and ends with a line containing "//".<br />
<br />
====Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json.gz)====<br />
This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the [https://bdsc.indiana.edu/ Bloomington Drosophila Stock Center], in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format [http://flybase.org/GAL4/freq_used_drivers.tsv here].<br />
<br />
===Aberrations===<br />
====Aberration data (Chado XML)====<br />
====Balancer data (Chado XML)====<br />
<br />
===Large dataset metadata===<br />
====Dataset metadata members (dataset_metadata_fb_*.tsv.gz)====<br />
This file lists all features that are associated with a dataset/collection (e.g., genes, cDNA clones, TF_binding_sites, Affymetrix probes).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dataset_Metadata_ID'''<br />
|The unique FlyBase ID for the dataset.<br />
|-<br />
|'''Dataset_Metadata_Name'''<br />
|The official FlyBase symbol for the dataset.<br />
|-<br />
|'''Item_ID'''<br />
|The unique FlyBase ID for the feature associated with this dataset.<br />
|-<br />
|'''Item_Name'''<br />
|The official FlyBase symbol for the feature associated with this dataset.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Clones===<br />
<br />
====Clone data (Chado XML)====<br />
<br />
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====<br />
The file reports basic cDNA clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of cDNA clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''dataset_metadata_name'''<br />
|Name of dataset associated with clone.<br />
|-<br />
|'''cDNA_accession(s)'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|'''EST_accession(s)'''<br />
|EMBL/GenBank/DDBJ EST accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====<br />
<br />
The file reports basic genomic clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of genomic clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''accession'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===References===<br />
====Combined reference data (Chado XML)====<br />
====FlyBase FBrf <=> PubMed ID <=> PMCID <=> DOI (fbrf_pmid_pmcid_doi_fb_*.tsv.gz)====<br />
<br />
This file lists all publications in the FlyBase bibliography that have a PubMed ID. Additional identifiers are listed as applicable.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBrf'''<br />
|The unique FlyBase ID for this publication.<br />
|-<br />
|'''PMID'''<br />
|The unique PubMed ID for this publication.<br />
|-<br />
|'''PMCID'''<br />
|The unique PubMed Central ID for this publication, if applicable.<br />
|-<br />
|'''DOI'''<br />
|The digital object identifier assigned to the publication.<br />
|-<br />
|'''pub_type'''<br />
|The publication type (for example, paper, review, erratum, abstract, book, etc.)<br />
|-<br />
|'''miniref'''<br />
|A short citation listing the first author, year of publication, journal, volume, issue and page numbers.<br />
|-<br />
|'''pmid_added'''<br />
|The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Drosophila researchers===<br />
Addresses of Drosophila researchers are copyrighted (GSA) material and only provided for official business of the Fly Board.<br />
<br />
===Map conversion tables===<br />
====Cytological <=> Sequence (genome-cyto-seq.txt)====<br />
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [[FlyBase:Computed_cytological_data|section G.5.1.]] of the Reference manual.<br />
<br />
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.<br />
<br />
The columns in the file are:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|Cytogenetic map position as described by Bridges.<br />
|-<br />
|'''-'''<br />
|First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|'''-'''<br />
|Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Cytological <=> Genetic (cytotable.txt)====<br />
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.<br />
<br />
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.<br />
<br />
<br />
====Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)====<br />
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 6 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Cytogenetic map position'''<br />
|Cytogenetic map position.<br />
|-<br />
|'''Genetic map position'''<br />
|Genetic map position.<br />
|-<br />
|'''Sequence coordinates (release 6)'''<br />
|Sequence coordinates (release 6) for the interval.<br />
|-<br />
|'''R6 conversion notes'''<br />
|<br />
|-<br />
|}<br />
<br />
<br />
An html version of this file is also available - see the [http://{{flybaseorg}}/static_pages/docs/cytotable3.html Map Conversion Table] page.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_fb_*.tsv)====<br />
This is identical to the file listed under the genes section above.<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Downloads_Overview&diff=170216FlyBase:Downloads Overview2019-01-14T17:03:25Z<p>Sian: /* Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json) */</p>
<hr />
<div>==Introduction==<br />
<br />
The "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page]" (referred to herein as the "Precomputed files" page) lists data files generated from the current release of FlyBase and links to the [ftp://ftp.flybase.net/releases/current/ current FTP repository]. Data from the previous five releases can be found on the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=archivedata3.html&title=Archived%20Releases Archived data files for recent releases]" page (referred to herein as the "Archived data" page), as well as links to servers hosting older releases of FlyBase, and all the release notes and news archives from FB2006_01. If you are looking for old data and cannot find it on the "Archived data" page please follow a link to the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
===Known issues===<br />
<br />
Safari does not connect properly to the FlyBase FTP site. You should be able to download individual files using Safari but you will not be able to browse the FTP repository.<br />
<br />
==The FTP archive==<br />
<br />
The "Main Data Set" section of the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Precomputed files]" page provides links to FlyBase FTP repository. The "Chado database" link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:<br />
<br />
$ psql -h chado.flybase.org -U flybase flybase<br />
<br />
The version running on this service is identical to the current web site release.<br />
<br />
The "Drosophila Data" section contains links to other sections of the FTP repository. The data can be accessed either by the version of FlyBase (The "[ftp://ftp.flybase.net/releases/current/ Current FTP repository]") or for sequence data by the annotation release of a particular Drosophila species (see the "[ftp://ftp.flybase.net/genomes/ Genomes FTP archive]")<br />
<br />
==General information about the available files==<br />
<br />
===File names===<br />
The first part of a filename always describes the content of the file, for example the file fbgn_annotation_ID_fb_2008_10.tsv.gz maps the primary FlyBase identifiers to the annotation symbols used for genes.<br />
<br />
Many of the precomputed data filenames also contain a release or version number. In the example above "fb_2008_10" denotes version FB2008_10 of FlyBase. Sequence data files, such as dmel-all-CDS-r5.13.fasta.gz, denote the annotation release that the data relates to as '-r5.13'. The 'r5' indicates the data is taken from the release 5 of the sequence assembly and the '13' after the decimal point specifies the annotation release.<br />
<br />
The following notation is used for different file formats: <br />
<br />
:'''Tab separated files''' are indicated by the extension ''''.tsv''''<br />
:'''[http://www.geneontology.org/GO.format.shtml#oboflat OBO format files]''', which are used for the ontologies, are denoted ''''.obo''''<br />
:'''Plain text''' files are given the extension ''''.txt''''<br />
:Files containing nucleic acid or polypeptide sequence data in the '''FASTA''' format are listed as ''''.fasta''''<br />
:'''GFF''' files include the suffix ''''.gff''''<br />
:'''GTF''' files include the suffix ''''.gtf''''<br />
:'''XML''' data files are denoted ''''.xml''''<br />
<br />
Most of the files listed on the "Precomputed files" page and the "Archived data" page are compressed with the [http://www.gzip.org/ GNU gzip] program. These files end with the suffix '.gz'. The ontology files are compressed in the ZIP file format, as indicated by the suffix '.zip'.<br />
<br />
===Accessing files===<br />
Files can be downloaded either directly through the web interface, or by using an ftp client such as wget to obtain the file from the FTP repository. Please note that at present Safari fails to connect to the FTP repository correctly, so we recommend that you use another browser if you wish to access the files through the web interface. The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file. Archived copies of the files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve this file for the FB2008_05 release, type:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
or more specifically:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_fb_2008_05.tsv.gz<br />
<br />
<br />
===Opening compressed files===<br />
Microsoft and Apple include built-in ZIP support in later versions of their operating systems. These files can also be opened with the free program [http://www.7-zip.org/ 7-zip].<br />
<br />
On OS X or Unix a GZIP compressed file can be extracted with the gunzip command. On a Windows machine we suggest that you use the program [http://www.7-zip.org/ 7-zip] to open these files, because several people have reported problems using WinZip. You should be able to open and read the resulting file with any text editor. <br />
<br />
<br />
==Types of files available==<br />
<br />
===XML files===<br />
<br />
These files are generated from the PostgreSQL Chado database for each release of FlyBase. The Chado XML files contain all the information used to generate the report pages and reflect the organization of the data in the database. The DTDs for these XML files, listing the structure of the files, are posted in the chado-xml directory of the FTP repository for each release. For the latest versions of the DTDs please see:<br />
<br />
ftp://ftp.flybase.net/releases/current/chado-xml/<br />
<br />
The XML files can also be obtained directly from the "Precomputed files" page by clicking on the "download" link under the ChadoXML heading in the appropriate section. The Chado XML files are available for genes, alleles, stocks, transcripts, polypeptides, insertions, transgenic (recombinant) constructs, aberrations, balancers, clones, and references.<br />
<br />
===Ontology files===<br />
<br />
The [http://{{flybaseorg}}/static_pages/docs/refman/refman-G.html#G.2. controlled vocabularies] (aka ontologies) used by FlyBase are available under the Ontology Terms section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page. Each controlled vocabulary is described in detail in [[FlyBase:Controlled vocabularies used by FlyBase|section G.2]]. of the Reference Manual. The files are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and are designed to be used with the free [http://www.oboedit.org/ OBO-Edit] tool.<br />
<br />
Controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects. On the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page the frozen versions of the controlled vocabularies used for the current release of FlyBase are available, and there are also links to the current 'live' versions maintained by the [http://www.obofoundry.org/ Open Biomedical Ontology] group.<br />
<br />
Frozen versions of the controlled vocabularies used for previous releases of FlyBase are available on the "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" page, and in the following directories of the FTP repository:<br />
<br />
ftp://ftp.flybase.net/releases/<RELEASE_NUMBER>/precomputed_files/ontologies/<br />
<br />
For example see:<br />
<br />
ftp://ftp.flybase.net/releases/FB2008_03/precomputed_files/ontologies/<br />
<br />
===FASTA files===<br />
<br />
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:<br />
<br />
'''dmel-all-<data type>-r<release-number>.fasta.gz'''<br />
<br />
or<br />
<br />
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''<br />
<br />
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome. <br />
<br />
{| class= "wikitable"<br />
!Data Type <br />
!Content Description<br />
|-<br />
|'''aligned ''' <br />
|The region of genomic sequence that analysis features align to.<br />
|-<br />
|'''CDS''' <br />
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.<br />
|-<br />
|'''chromosome'''<br />
|The sequence of each chromosome arm.<br />
|-<br />
|'''clones''' <br />
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.<br />
|-<br />
|'''exon ''' <br />
|The sequence of each exon split up into individual FASTA records.<br />
|-<br />
|'''five_prime_UTR'''<br />
|The sequence of 5' untranslated regions.<br />
|-<br />
|'''gene''' <br />
|The sequence of the gene span.<br />
|-<br />
|'''gene_extended2000''' <br />
|The sequence of the gene span with 2000 base pairs added upstream and downstream.<br />
|-<br />
|'''intergenic'''<br />
|The sequence of chromosomal regions between genes that do not contain known gene models.<br />
|-<br />
|'''intron''' <br />
|The sequence of each intron split up into individual FASTA records.<br />
|-<br />
|'''miRNA''' <br />
|The sequence of transcripts that are typed as micro RNAs.<br />
|-<br />
|'''miscRNA''' <br />
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.<br />
|-<br />
|'''ncRNA''' <br />
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).<br />
|-<br />
|'''predicted''' <br />
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.<br />
|-<br />
|'''pseudogene''' <br />
|The sequence of transcripts that are typed as pseudogenes.<br />
|-<br />
|'''sequence_features''' <br />
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.<br />
|-<br />
|'''synteny'''<br />
|The sequence of syntenic regions between two species.<br />
|-<br />
|'''three_prime_UTR'''<br />
|The sequence of 3' untranslated regions.<br />
|-<br />
|'''transcript'''<br />
|The sequence of transcripts that are typed as messenger RNAs (mRNA).<br />
|-<br />
|'''translation''' <br />
|The resulting protein sequence from protein coding transcripts.<br />
|-<br />
|'''transposon'''<br />
|The sequence of transposable elements.<br />
|-<br />
|'''tRNA''' <br />
|The sequence of transcripts that are typed as transfer RNAs (tRNA).<br />
|}<br />
<br />
<br />
====FASTA header format====<br />
<br />
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format<br />
<br />
'''field_name=value;'''<br />
<br />
Multiple field values are separated by commas<br />
<br />
'''field_name=value1,value2;'''<br />
<br />
This table describes some of the field names found in our FASTA headers <br />
<br />
{|class = "wikitable"<br />
<br />
!Field Name<br />
!Description<br />
|-<br />
|'''type''' <br />
|The feature type of the FASTA sequence record.<br />
|-<br />
|'''loc''' <br />
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.<br />
|-<br />
|'''ID''' <br />
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.<br />
|-<br />
|'''name'''<br />
|The name or symbol of the feature.<br />
|-<br />
|'''dbxref'''<br />
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.<br />
|-<br />
|'''MD5'''<br />
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.<br />
|-<br />
|'''length'''<br />
|The length of the sequence found in the FASTA record.<br />
|-<br />
|'''release'''<br />
|The release number denotes the annotation release which this FASTA record corresponds to.<br />
|-<br />
|'''species'''<br />
|The species abbreviation that this FASTA record corresponds to.<br />
|}<br />
<br />
<br />
===GFF files===<br />
<br />
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features. The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gff/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gff/<br />
<br />
For melanogaster, there are 3 GFF files distributed, they include:<br />
<br />
:'''dmel-all-r<release-number>.gff.gz'''<br />
::Contains all chromosome arms<br />
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''<br />
::Same as above except all match and match_part features have been removed<br />
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''<br />
::Contains only a single chromosome arm as identifed by the filename<br />
<br />
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues. <br />
<br />
===GTF files===<br />
<br />
The FlyBase GTF files follow the [http://mblab.wustl.edu/GTF22.html GTF v2.2] specification. The GTF files contain feature line definitions for gene models. The GTF are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gtf/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gtf/<br />
<br />
===Precomputed data text files===<br />
<br />
Precomputed data files that contain useful sets of data are generated for every release of FlyBase. For example, the file fbgn_NAseq_Uniprot_fb_2008_10.tsv.gz contains the mapping between valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] and the corresponding nucleic acid and protein accession numbers used by DDBJ/EMBL/GenBank and UniprotKB/Swiss-Prot/TrEMBL. These files can be found under the "Other" heading of each section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" and "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" pages, and are also available under the precomputed_files directory of each FlyBase release in the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.<br />
<br />
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.<br />
<br />
Each precomputed data file available for download on the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page contains the complete data set for the FlyBase release. Please note, if you are only looking for information on a defined subset of genes, or other FlyBase data type, you can query the current set of precomputed data files through the [http://{{flybaseorg}}/batchdownload Batch Download] tool to obtain the data you require. This approach is described in more detail in [https://wiki.flybase.org/wiki/FlyBase:Batch_Download this] help document.<br />
<br />
==Contents of the precomputed data text files listed by section==<br />
<br />
===Main data set===<br />
<br />
====Postgres Chado database dump====<br />
=====Chado database (ftp://ftp.flybase.net/releases/current/psql)=====<br />
The entire SQL Chado database is available for download. Follow the "README" directions herein.<br />
<br />
====Drosophila data====<br />
=====Current FTP repository (ftp://ftp.flybase.net/releases/current/)=====<br />
All files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Current Chado-XML repository (ftp://ftp.flybase.net/releases/current/chado-xml)=====<br />
All Chado XML files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Genomes FTP archive (ftp://ftp.flybase.net/genomes/)=====<br />
All FlyBase genome and genome annotation files are available for various Drosophila species. Formats include Chado XML, DNA, FASTA, GFF and GTF. Files from both the current release and previous FlyBase releases are offered. For release FB2018_05 and earlier, data is available for each of the original 12 sequenced Drosophila species. From release FB2018_06 onward, data is available only for D. melanogaster, D. simulans, D. ananassae, D. pseudoobscura and D. virilis.<br />
<br />
===Synonyms===<br />
<br />
====FlyBase Synonyms (fb_synonym_*.tsv)====<br />
The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).<br />
<br />
The file includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
* genes from drosophilid species and genes from non-drosophilids that have been introduced into transgenic flies<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''primary_FBid''' <br />
|Primary FlyBase identifier for the object.<br />
|-<br />
|'''organism_abbreviation''' <br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin.<br />
|-<br />
|'''current_symbol'''<br />
|Current symbol used in FlyBase for the object.<br />
|-<br />
|'''current_fullname''' <br />
|Current full name used in FlyBase for the object.<br />
|-<br />
|'''fullname_synonym(s)''' <br />
|Non-current full name(s) associated with the object (comma separated values).<br />
|-<br />
|'''symbol_synonym(s)'''<br />
|Non-current symbol(s) associated with the object (comma separated values).<br />
|-<br />
|}<br />
<br />
===Genes===<br />
<br />
====Genes data (Chado XML)====<br />
<br />
====Genetic interaction table (gene_genetic_interactions_*.tsv)====<br />
The file reports the summary of gene-level genetic interactions in FlyBase. This data is computed from the allele-level genetic interaction data captured by FlyBase curators.<br />
<br />
The file includes information for Dmel genes only.<br />
<br />
Interactions involving any of the following kinds of allele are considered when the gene-level genetic interaction data is computed:<br />
<br />
* classical mutations<br />
* alleles carried on transgenic constructs<br />
* loss-of-function mutations<br />
* gain-of-function mutations<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Starting_gene(s)_symbol''' <br />
|Current FlyBase symbol of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Starting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Interacting_gene(s)_symbol'''<br />
|Current FlyBase symbol of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interacting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interaction_type''' <br />
|Type of interaction observed, either 'suppressible' or 'enhanceable'.<br />
|-<br />
|'''Publication_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if the same genetic interaction has been reported in multiple references, multiple rows will exist for that genetic interaction in the file.<br />
<br />
* 'suppressible' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are suppressed by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
* 'enhanceable' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are enhanced by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
''e.g.''<br />
<br />
Pten&emsp;FBgn0026379&emsp;Akt1&emsp;FBgn0010379&emsp;suppressible&emsp;FBrf0127089<br />
<br />
indicates that phenotype(s) caused by a mutation of Pten are suppressed by a mutation of Akt1.<br />
<br />
* For cases where multiple genes are simultaneously mutated in either (or both) the starting and interacting genotype, then the genes involved are separated by a '|' in the relevant columns. In this case, the order of the list of symbols and of the list of ids in columns 1 and 2, or in columns 3 and 4 respectively are the same, so that the FBgn corresponding to the symbol for each gene can easily be identified.<br />
<br />
''e.g.''<br />
<br />
robo1|sli&emsp;FBgn0005631|FBgn0264089&emsp;RhoGAP93B&emsp;FBgn0038853&emsp;enhanceable&emsp;FBrf0191476<br />
<br />
indicates that:<br />
* phenotype(s) caused by a robo1, sli double mutant combination are enhanced by a mutation of RhoGAP93B.<br />
* FBgn0005631 corresponds to robo1, FBgn0264089 corresponds to sli<br />
<br />
<br />
<br />
====RNA-Seq RPKM values (gene_rpkm_report_fb_*.tsv.gz)====<br />
This file reports gene expression values based on RNA-Seq experiments, calculated as reads per kilobase per million reads (RPKM). RPKM values are calculated only for the unique exonic regions of the gene (excluding segments that overlap other genes), except for genes derived from dicistronic/polycistronic transcripts, in which case all exon regions are used in the RPKM expression calculation.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Release_ID'''<br />
|The D. melanogaster annotation set version from which the gene model used in the analysis derives.<br />
|-<br />
|'''FBgn#'''<br />
|The unique FlyBase gene ID for this gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|The official FlyBase symbol for this gene.<br />
|-<br />
|'''Parent_library_FBlc#'''<br />
|The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''Parent_library_name'''<br />
|The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''RNASource_FBlc#'''<br />
|The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RNASource_name'''<br />
|The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RPKM_value'''<br />
|The RPKM expression value for the gene in the specified RNA-Seq experiment.<br />
|-<br />
|'''Bin_value'''<br />
|The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression).<br />
|-<br />
|'''Unique_exon_base_count'''<br />
|The number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts.<br />
|-<br />
|'''Total_exon_base_count'''<br />
|The number of bases in all exons of this gene.<br />
|-<br />
|'''Count_used'''<br />
|Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Physical interaction table (physical_interactions_fb_*.tsv.gz)====<br />
This file reports unique gene pairs with curated support for some type of physical interaction. The file does not currently distinguish between genes that are involved in protein-protein or RNA-protein interactions (or both).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_FBgn1'''<br />
|The unique FlyBase gene ID for the first gene of the interacting pair.<br />
|-<br />
|'''gene_symbol1'''<br />
|The official FlyBase symbol for the first gene of the interacting pair.<br />
|-<br />
|'''gene_FBgn2'''<br />
|The unique FlyBase gene ID for the second gene of the interacting pair.<br />
|-<br />
|'''gene_symbol2'''<br />
|The official FlyBase symbol for the second gene of the interacting pair.<br />
|-<br />
|'''FBrf(s)'''<br />
|The unique FlyBase IDs for the publications supporting this interaction.<br />
|-<br />
|'''FBig_id'''<br />
|The unique FlyBase ID for this pairwise interaction.<br />
|-<br />
|'''#_reported_interactions'''<br />
|The number of distinct experiments in support of this interaction.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction MITAB file (physical_interactions_mitab_fb_*.tsv.gz)====<br />
This file reports each individual experiment curated by FlyBase that supports a physical interaction between two gene products. There can be multiple experiments (multiple rows in the file) between products of the same gene pair. Interaction molecule types currently curated are protein-protein, protein-RNA or RNA-RNA. <br />
<br />
This file is in PSI-MI TAB format, a tab-delimited format developed by the HUPO Proteomics Standards Initiative (PSI) Molecular Interactions (MI) working group to facilitate interactomics data comparison and exchange. Details on the general MITAB format can be found [https://psicquic.github.io/MITAB27Format.html here]. The file makes use of the Molecular Interactions ontology which can be searched or browsed [https://www.ebi.ac.uk/ols/ontologies/mi here]. Fields are filled with “-” if values are missing or not relevant.<br />
<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading<br />
!General format <br />
!FlyBase example<br />
!Content description<br />
|-<br />
|'''1'''<br />
|'''ID(s) Interactor A'''<br />
|database:identifier<br />
|flybase:FBgn0002121<br />
|The unique Flybase identifier for the first gene of the interacting pair.<br />
|-<br />
|'''2'''<br />
|'''ID(s) Interactor B'''<br />
|”<br />
|”<br />
|The unique Flybase identifier for the second gene of the interacting pair.<br />
|-<br />
|'''3'''<br />
|'''Alt ID(s) Interactor A'''<br />
|database:identifier<br />
|<nowiki>flybase:CG2671|entrez gene/locuslink:33156</nowiki><br />
|<nowiki>The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|”.</nowiki><br />
|-<br />
|'''4'''<br />
|'''Alt ID(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''5'''<br />
|'''Alias(es) Interactor A'''<br />
|database:name(alias type)<br />
|flybase:l(2)gl(gene name)<br />
|The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.<br />
|-<br />
|'''6'''<br />
|'''Alias(es) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''7'''<br />
|'''Interaction Detection Method(s)'''<br />
|ontology:identifier(method name)<br />
|psi-mi:"MI:0006"(anti bait coimmunoprecipitation)<br />
|The assay used to detect the interaction, taken from the psi-mi ontology.<br />
|-<br />
|'''8'''<br />
|'''Publication 1st Author(s)'''<br />
|surname initial(s) (publication year)<br />
|Betschinger K. (2003)<br />
|The first author and year of the publication where the interaction is described.<br />
|-<br />
|'''9'''<br />
|'''Publication ID(s)'''<br />
|database:identifier<br />
|<nowiki>flybase:FBrf0157155|pubmed:12629552</nowiki><br />
|<nowiki>The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.</nowiki><br />
|-<br />
|'''10'''<br />
|'''Taxid Interactor A'''<br />
|taxid:identifier<br />
|taxid:7227("Drosophila melanogaster")<br />
|The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.<br />
|-<br />
|'''11'''<br />
|'''Taxid Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''12'''<br />
|'''Interaction Type(s)'''<br />
|ontology:identifier(interaction type)<br />
|psi-mi:"MI:0915"(physical association)<br />
|Taken from the psi-mi ontology. Most often “physical association” for FlyBase.<br />
|-<br />
|'''13'''<br />
|'''Source Database(s)'''<br />
|ontology:identifier(database name)<br />
|psi-mi:"MI:0478"(flybase)<br />
|All interactions are curated by FlyBase.<br />
|-<br />
|'''14'''<br />
|'''Interaction Identifier(s)'''<br />
|database:identifier<br />
|flybase:FBrf0157155-13.coIP.WB<br />
|The unique FlyBase identifier for this interaction.<br />
|-<br />
|'''15'''<br />
|'''Confidence Value(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''16'''<br />
|'''Expansion Method(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''17'''<br />
|'''Biological Role(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''18'''<br />
|'''Biological Role(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''19'''<br />
|'''Experimental Role(s) Interactor A'''<br />
|ontology:identifier(experimental role name)<br />
|psi-mi:"MI:0496"(bait)<br />
|The role played by the interactor in the experiment. Taken from the psi-mi ontology.<br />
|-<br />
|'''20'''<br />
|'''Experimental Role(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''21'''<br />
|'''Type(s) Interactor A'''<br />
|ontology:identifier(interactor type name)<br />
|psi-mi:"MI:0326"(protein)<br />
|The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.<br />
|-<br />
|'''22'''<br />
|'''Type(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''23'''<br />
|'''Xref(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''24'''<br />
|'''Xref(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''25'''<br />
|'''Interaction Xref(s)'''<br />
|database:identifier<br />
|flybase:FBig0000000103<br />
|<nowiki>Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.</nowiki><br />
|-<br />
|'''26'''<br />
|'''Annotation(s) Interactor A'''<br />
|topic:text<br />
|isoform-comment:a isoform<br />
|Information on whether the interaction is specific to a particular interactor isoform.<br />
|-<br />
|'''27'''<br />
|'''Annotation(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''28'''<br />
|'''Interaction Annotation(s)'''<br />
|topic:text<br />
|molecular source:Source was cell extract of S2 cell line; bait produced from endogenous gene; prey produced from endogenous gene.|comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.<br />
|Describes the source(s) of the interaction participants and includes free text comments about the interaction.<br />
|-<br />
|'''29'''<br />
|'''Host Organism(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''30'''<br />
|'''Interaction Parameters'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''31'''<br />
|'''Creation Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''32'''<br />
|'''Update Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''33'''<br />
|'''Checksum Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''34'''<br />
|'''Checksum Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''35'''<br />
|'''Interaction Checksum'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''36'''<br />
|'''Negative'''<br />
|<br />
|FALSE<br />
|All interactions in FlyBase are positive.<br />
|-<br />
|'''37'''<br />
|'''Feature(s) Interactor A'''<br />
|feature_type:range(text)<br />
|sufficient binding region:aa 1-58(N-terminal region)<br />
|Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.<br />
|-<br />
|'''38'''<br />
|'''Feature(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''39'''<br />
|'''Stoichiometry Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''40'''<br />
|'''Stoichiometry Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''41'''<br />
|'''Identification Method(s) Participant A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''42'''<br />
|'''Identification Method(s) Participant B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|}<br />
<br />
<br />
====Functional complementation table (gene_functional_complementation_*.tsv)====<br />
<br />
This file reports when functional complementation of Dmel genes by non-Dmel orthologs has been observed. This data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature. The file contains a list of gene Dmel - to - non-Dmel-ortholog gene pairs where a transgenic construct/mutant allele of the non-Dmel ortholog has been shown to at least partially suppress mutant phenotype(s) of an allele of the Dmel gene.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''Dmel gene (symbol)'''<br />
|Current FlyBase symbol of Dmel gene.<br />
|-<br />
|'''2'''<br />
|'''Dmel gene (FBgn)'''<br />
|Current FlyBase identifier (FBgn#) of Dmel gene in column 1.<br />
|-<br />
|'''3'''<br />
|'''Functionally complementing ortholog (symbol)'''<br />
|Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''4'''<br />
|'''Functionally complementing ortholog (FBgn#)'''<br />
|Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''5'''<br />
|'''Supporting_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if multiple references support the same functional complementation statement, multiple rows will exist for that statement in the file.<br />
<br />
<br />
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====<br />
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, UniProtKB/SwissProt/TrEMBL protein accessions, NCBI Entrez gene IDs and NCBI RefSeq transcript and protein accessions associated with FlyBase genes.<br />
<br />
The file includes:<br />
* nuclear genes with sequence accession numbers<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes without sequence accession numbers<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''2'''<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''3'''<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''4'''<br />
|'''nucleotide_accession'''<br />
|EMBL/GenBank/DDBJ nucleotide accession associated with the gene.<br />
|-<br />
|'''5'''<br />
|'''na_based_protein_accession'''<br />
|EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column<br />
|-<br />
|'''6'''<br />
|'''UniprotKB/Swiss-Prot/TrEMBL_accession'''<br />
|UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.<br />
|-<br />
|'''7'''<br />
|'''EntrezGene_ID'''<br />
|NCBI Entrez ID associated with the gene.<br />
|-<br />
|'''8'''<br />
|'''RefSeq_transcripts'''<br />
|NCBI RefSeq transcript accession associated with the gene.<br />
|-<br />
|'''9'''<br />
|'''RefSeq_proteins'''<br />
|NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.<br />
<br />
* A single row contains '''only''' information about an EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession '''or''' an NCBI Entrez gene ID '''or''' an NCBI RefSeq transcript accession.<br />
<br />
* For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 4 ('nucleotide_accession'). If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 4, this protein accession is listed in column 5 ('na_based_protein_accession'). In this case, columns 6, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 6 ('UniprotKB/Swiss-Prot/TrEMBL_accession'). In this case, columns 4, 5, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI Entrez gene, an ID associated with the gene is listed in column 7 ('EntrezGene_ID'). In this case, columns 4, 5, 6, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI RefSeq accession, a transcript accession associated with the gene is listed in column 8 ('RefSeq_transcripts'). If there is also an NCBI RefSeq protein accession associated with that gene '''and''' with the transcript accession in column 8, this protein accession is listed in column 9 ('RefSeq_proteins'). In this case, columns 4, 5, 6 and 7 are always empty.<br />
<br />
<br />
<br />
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====<br />
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''secondary_FBgn#(s)'''<br />
|Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).<br />
|-<br />
|'''annotation_ID'''<br />
|Current annotation identifier associated with the gene.<br />
|-<br />
|'''secondary_annotation_ID(s)'''<br />
|Secondary annotation identifier(s) associated with the gene (comma separated values).<br />
|-<br />
|}<br />
Notes:<br />
<br />
* If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702). <br />
<br />
<br />
<br />
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====<br />
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.<br />
<br />
The file includes:<br />
* non-melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* ''D. melanogaster'' genes<br />
* non-melanogaster genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''gene_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GLEANR_ID'''<br />
|GLEANR identifier assigned by the AAA Consortium.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====<br />
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.<br />
<br />
The file includes:<br />
* genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FlyBase_FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FlyBase_FBtr'''<br />
|Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.<br />
|-<br />
|'''FlyBase_FBpp'''<br />
|Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript and the polypeptide it encodes (if relevant). Thus if a gene encodes multiple isoforms, multiple rows with exist for that gene in the file.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====<br />
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.<br />
<br />
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.<br />
<br />
The file includes the following '''Dmel''' genes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
Notes:<br />
<br />
* Each line of the file '''can contain many''' tab separated columns:<br />
<br />
* '''The first column of a line''' contains the valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] of a gene.<br />
* '''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====<br />
The file is generated from the location of Affy2 oligos exactly as [[FlyBase:FilesOverview#5.2.6|described for Affy1 oligos]] above.<br />
<br />
<br />
<br />
====Genes GO data (gene_association.fb)====<br />
The file contains the [http://www.geneontology.org/ Gene Ontology] (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.<br />
<br />
The file includes the following Dmel genes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
The columns of the file are described in [[FlyBase:Gene Ontology (GO) Annotation|section G.3.1.]] of the Reference manual.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_*.tsv)====<br />
The file reports available localization information for FlyBase genes.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''current_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBid'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''recombination_loc'''<br />
|recombination map location.<br />
|-<br />
|'''cytogenetic_loc'''<br />
|cytogenetic location.<br />
|-<br />
|'''sequence_loc'''<br />
|genomic location.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Automated gene summaries (automated_gene_summaries.tsv)====<br />
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|FlyBase ID. The Valid FlyBase identifier number for the gene.<br />
|-<br />
|'''-'''<br />
|The gene summary as a string of plain text.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Gene Snapshots (gene_snapshots_*.tsv)====<br />
The file contains in plain text the gene snapshot information visible on gene report pages.<br />
<br />
It includes only Dmel protein coding genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier number for the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase symbol of the gene.<br />
|-<br />
|'''GeneName'''<br />
|Current FlyBase name of the gene.<br />
|-<br />
|'''datestamp'''<br />
|Date on which the information was last reviewed.<br />
|-<br />
|'''gene_snapshot_text'''<br />
|Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Unique protein isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their unique protein isoforms.<br />
<br />
The file includes:<br />
* melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* melanogaster genes not located to the sequence<br />
* non-melanogaster genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FB_gene_symbol'''<br />
|Current FlyBase gene symbol of the gene.<br />
|-<br />
|'''representative_protein'''<br />
|Current FlyBase protein symbol of the representative protein isoform.<br />
|-<br />
|'''identical_protein(s)'''<br />
|Current FlyBase protein symbol(s) of identical protein isoforms.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNA genes (TSV) (ncRNA_genes_fb_*.tsv.gz)====<br />
This file reports all genes encoding ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in TSV format. Pseudogenes are excluded.<br />
<br />
Columns are:<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''accession_id'''<br />
|INSDC accession ID.<br />
|-<br />
|'''FB_gene_ID'''<br />
|Current FlyBase gene identifier (FBgn#).<br />
|-<br />
|'''species_FB_annotation_ID(locus_tag)'''<br />
|Current FlyBase annotation ID, in the form "<species abbreviation>_<annotation_ID>", which equates to the 'locus tag' field in INSDC records.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Gene groups===<br />
====Gene group data (gene_group_data_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with their hierarchical relationships (where relevant) and member genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''Parent_FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Parent_FB_group_symbol'''<br />
|Current FlyBase symbol of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Group_member_FB_gene_id'''<br />
|Current FlyBase identifier (FBgn##) of member gene (if terminal group).<br />
|-<br />
|'''Group_member_FB_gene_symbol'''<br />
|Current FlyBase symbol of member gene (if terminal group).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Where groups are arranged into hierarchies:<br />
** the member genes are only associated with the terminal subgroups,<br />
** the immediate parent of any subgroup is identified in the ‘Parent_FB_group_id' and 'Parent_FB_group_symbol' columns.<br />
<br />
* Separate lines are used for each member gene, meaning that each terminal group is listed multiple times (equal to the number of member genes).<br />
<br />
<br />
<br />
====Gene groups with HGNC IDs (gene_groups_HGNC_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with the corresponding HGNC 'gene family' ID (where relevant).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''HGNC_family_ID'''<br />
|HGNC ID of equivalent human 'gene family'.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* The absence of an HGNC_family_ID entry indicates there is no equivalent HGNC gene family for that FlyBase gene group.<br />
<br />
* Because of different sub-group structures (etc), a single HGNC family may be associated with multiple FlyBase gene groups.<br />
<br />
* Similarly, a single FlyBase gene group may be associated with multiple HGNC gene families - these are shown on separate lines.<br />
<br />
<br />
<br />
===Alleles and Stocks===<br />
====Allele data (Chado XML)====<br />
<br />
====Stock data (Chado XML)====<br />
<br />
====Stock data (stocks_*.tsv.gz)====<br />
This file reports genetic components and related information about Stocks in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
!Example<br />
|-<br />
|'''FBst'''<br />
|The unique identifier assigned to this stock by FlyBase.<br />
|FBst0000002<br />
|-<br />
|'''collection_short_name'''<br />
|A short name for the stock collection that holds the stock.<br />
|Bloomington<br />
|-<br />
|'''stock_type_cv'''<br />
|The controlled vocabulary term and unique identifier that describe the state of the stock.<br />
|living stock ; FBsv:0000002<br />
|-<br />
|'''species'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of the stock.<br />
|Dmel<br />
|-<br />
|'''FB_genotype'''<br />
|Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.<br />
|w[*]; betaTub60D[2] Kr[If-1]/CyO<br />
|-<br />
|'''description'''<br />
|Genetic components of the stock as provided to FlyBase by the collection that holds the stock.<br />
|FlyTrap: ZCL1796 III<br />
|-<br />
|'''stock_number'''<br />
|The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.<br />
|110818<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genetic interactions (allele_genetic_interactions_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''interaction'''<br />
|Interaction information associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single interaction from a single reference. Thus if multiple genetic interactions have been reported for a given allele, or if multiple references report the same interaction for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Phenotypic data (allele_phenotypic_data_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''phenotype'''<br />
|Phenotypic data associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes: <br />
<br />
* Each row contains information about a single phenotype from a single reference. Thus if multiple phenotypes have been reported for a given allele, or if multiple references report the same phenotype for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Alleles <=> Genes (fbal_to_fbgn_fb_*.tsv)====<br />
This file reports the relationship between gene identifiers and the identifiers used for alleles of these genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''AlleleID'''<br />
|Current FlyBase identifier (FBal#) of the allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current symbol of the allele.<br />
|-<br />
|'''GeneID'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Orthologs===<br />
<br />
====Drosophila Orthologs (dmel_orthologs_in_drosophila_species_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their orthologs in other sequenced Drosophila genomes, as determined by OrthoDB. (The version of OrthoDB currently being used is shown in the 'Orthologs' -> 'Orthologs (via OrthoDB)' section of a Gene Report.)<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Ortholog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_Arm/Scaffold'''<br />
|Arm upon which the non-melanogaster orthologous gene is localized.<br />
|-<br />
|'''Ortholog_Location'''<br />
|Location of non-melanogaster orthologous gene on the arm.<br />
|-<br />
|'''Ortholog_Strand'''<br />
|Strand of non-melanogaster orthologous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''OrthoDB_Group_ID'''<br />
|OrthoDB orthology group ID to which the pair-wise association belongs.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association beween a ''D. melanogaster'' gene and a non-melanogaster ortholog. Thus, multiple rows exist for each ''D. melanogaster'' gene in the file.<br />
<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dmel_gene_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Dmel_gene_symbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Human_gene_HGNC_ID'''<br />
|HGNC ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_OMIM_ID'''<br />
|OMIM ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_symbol'''<br />
|HGNC gene symbol of orthologous human gene.<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|'''OMIM_Phenotype_IDs'''<br />
|OMIM Phenotype ID of orthologous human gene (comma separated values).<br />
|-<br />
|'''OMIM_Phenotype_IDs[name]'''<br />
|OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets). Multiple phenotype[name] entries are separated by a comma.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Human disease===<br />
<br />
====Human disease model data (allele_human_disease_model_data_fb_*.tsv.gz)====<br />
This file reports all experimental-based disease model annotations, associated with alleles, that have been curated for ''D. melanogaster''. 'Alleles' encompasses both classical alleles and transgenic alleles; the latter may relate to transgenic constructs of ''D. melanogaster'' genes or non-''D. melanogaster'' genes, often human genes. These are the data reported in the "Human Disease Model Data" -> "Disease Ontology" section of the Allele Report, which are repeated in the "Human Disease Model Data" -> "Alleles Reported to Model Human Disease (Disease Ontology)" section of the Gene Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBal_ID'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current FlyBase symbol of allele.<br />
|-<br />
|'''DOID_qualifier'''<br />
|Annotation qualifier - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.<br />
|-<br />
|'''DOID_term'''<br />
|Disease Ontology term.<br />
|-<br />
|'''DOID_ID'''<br />
|Disease Ontology ID.<br />
|-<br />
|'''Evidence/interacting_alleles'''<br />
|Evidence code, with interacting allele(s) where appropriate. Evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma.<br />
|-<br />
|'''Reference_FBid'''<br />
|Current FlyBase identifier (FBrf#) of the publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
This is identical to the file of the same name listed under the 'Orthologs' section above. <br />
<br />
<br />
<br />
===Nomenclature===<br />
<br />
====Species abbreviation list (species-ab.gz)====<br />
<br />
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.<br />
<br />
There are 8 columns of data in the file, each separated by " | ".<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Internal_id'''<br />
|The Primary [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the organism.<br />
|-<br />
|'''Taxgroup'''<br />
|A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".<br />
|-<br />
|'''Abbreviation'''<br />
|The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.<br />
|-<br />
|'''Genus'''<br />
|The genus name of the organism.<br />
|-<br />
|'''Species name'''<br />
|The species name of the organism.<br />
|-<br />
|'''Common name'''<br />
|The common name of the organism. This column may be blank.<br />
|-<br />
|'''Comment'''<br />
|A free text field for additional comments. This column may be blank.<br />
|-<br />
|'''Ncbi-taxon-id'''<br />
|The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.<br />
|-<br />
|}<br />
<br />
An html version of this file is also available - see the [[FlyBase:Abbreviations|Species Abbreviations]] page.<br />
<br />
<br />
<br />
===Ontology Terms===<br />
====Frozen files used for this release of FlyBase====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
* FBdv: fly_development<br />
* FBcv: flybase controlled vocabulary<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
====Current 'Live' Files====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_anatomy.obo' version''<br />
* FBdv: fly_development<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_development.obo' version''<br />
* FBcv: flybase controlled vocabulary<br />
''Note: link points to the ontology version fbcv-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'flybase_controlled_vocabulary.obo' version''<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
===Genomes: Annotation and Sequence===<br />
====All Sequenced Drosophila Species====<br />
<br />
Links are available to the following FTP repositories:<br />
<br />
* Current FTP repository<br />
* Current FastA repository<br />
* Current GFF repository<br />
<br />
* FTP archive (previous releases)<br />
<br />
* Current list of individual FASTA files<br />
* Current list of individual GFF files<br />
<br />
For release FB2018_06 onward, the above links are available for the following sequenced Drosophila species:<br />
<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila melanogaster<br />
|Dmel<br />
|-<br />
|Drosophila ananassae<br />
|Dana<br />
|-<br />
|Drosophila pseudoobscura pseudoobscura<br />
|Dpse<br />
|-<br />
|Drosophila simulans<br />
|Dsim<br />
|-<br />
|Drosophila virilis<br />
|Dvir<br />
|-<br />
|}<br />
<br />
<br />
For earlier archived releases, the above links are also available for these additional species (other members of the original 12 sequenced Drosophila species):<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila erecta<br />
|Dere<br />
|-<br />
|Drosophila grimshawi<br />
|Dgri<br />
|-<br />
|Drosophila mojavensis<br />
|Dmoj<br />
|-<br />
|Drosophila persimilis<br />
|Dper<br />
|-<br />
|Drosophila sechellia<br />
|Dsec<br />
|-<br />
|Drosophila willistoni<br />
|Dwil<br />
|-<br />
|Drosophila yakuba<br />
|Dyak<br />
|-<br />
|}<br />
<br />
===Transcripts and Polypeptides===<br />
<br />
====Transcript data (Chado XML)====<br />
<br />
====Polypeptide data (Chado XML)====<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Transposons, Transgenic Constructs, and Insertions===<br />
<br />
====Insertions (Chado XML)====<br />
====Transgenic Constructs (Chado XML)====<br />
<br />
<br />
====Transgenic construct maps (construct_maps.zip)====<br />
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the respective recombinant construct or transgenic transposon.<br />
<br />
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.<br />
<br />
====Map data for insertions (insertion_mapping_*.tsv)====<br />
The insertion mapping table reports available localization information for '''Dmel''' insertions.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''insertion_symbol'''<br />
|Current symbol of insertion.<br />
|-<br />
|'''FBti#'''<br />
|Current FlyBase identifier (FBti#) of insertion<br />
.<br />
|-<br />
|'''genomic_location'''<br />
|Genomic location of insertion.<br />
|-<br />
|'''range'''<br />
|Range (t/f) indicates whether genomic location is range or single base.<br />
|-<br />
|'''orientation'''<br />
|Orientation (1/0) indicates orientation of insertion on chromosome.<br />
|-<br />
|'''estimated_cytogenetic_location'''<br />
|Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.<br />
|-<br />
|'''observed_cytogenetic_location'''<br />
|Observed cytogenetic location reported in the literature.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====<br />
This is a file of 'canonical' sequences of the transposable elements from Drosophila maintained by M. Ashburner.<br />
<br />
The first section of the file outlines the history and revisions to the file and also lists the current set of elements, their size and whether the subsequent sequence data is complete.<br />
<br />
The second section of the file, which is separated from the first by a line of "_" characters contains the sequence data of all the elements in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL format]. The record for each element starts with a line prefixed by "ID" and ends with a line containing "//".<br />
<br />
====Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json.gz)====<br />
This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the Bloomington Drosophila Stock Center, in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format [http://flybase.org/GAL4/freq_used_drivers.tsv here].<br />
<br />
===Aberrations===<br />
====Aberration data (Chado XML)====<br />
====Balancer data (Chado XML)====<br />
<br />
===Large dataset metadata===<br />
====Dataset metadata members (dataset_metadata_fb_*.tsv.gz)====<br />
This file lists all features that are associated with a dataset/collection (e.g., genes, cDNA clones, TF_binding_sites, Affymetrix probes).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dataset_Metadata_ID'''<br />
|The unique FlyBase ID for the dataset.<br />
|-<br />
|'''Dataset_Metadata_Name'''<br />
|The official FlyBase symbol for the dataset.<br />
|-<br />
|'''Item_ID'''<br />
|The unique FlyBase ID for the feature associated with this dataset.<br />
|-<br />
|'''Item_Name'''<br />
|The official FlyBase symbol for the feature associated with this dataset.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Clones===<br />
<br />
====Clone data (Chado XML)====<br />
<br />
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====<br />
The file reports basic cDNA clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of cDNA clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''dataset_metadata_name'''<br />
|Name of dataset associated with clone.<br />
|-<br />
|'''cDNA_accession(s)'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|'''EST_accession(s)'''<br />
|EMBL/GenBank/DDBJ EST accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====<br />
<br />
The file reports basic genomic clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of genomic clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''accession'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===References===<br />
====Combined reference data (Chado XML)====<br />
====FlyBase FBrf <=> PubMed ID <=> PMCID <=> DOI (fbrf_pmid_pmcid_doi_fb_*.tsv.gz)====<br />
<br />
This file lists all publications in the FlyBase bibliography that have a PubMed ID. Additional identifiers are listed as applicable.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBrf'''<br />
|The unique FlyBase ID for this publication.<br />
|-<br />
|'''PMID'''<br />
|The unique PubMed ID for this publication.<br />
|-<br />
|'''PMCID'''<br />
|The unique PubMed Central ID for this publication, if applicable.<br />
|-<br />
|'''DOI'''<br />
|The digital object identifier assigned to the publication.<br />
|-<br />
|'''pub_type'''<br />
|The publication type (for example, paper, review, erratum, abstract, book, etc.)<br />
|-<br />
|'''miniref'''<br />
|A short citation listing the first author, year of publication, journal, volume, issue and page numbers.<br />
|-<br />
|'''pmid_added'''<br />
|The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Drosophila researchers===<br />
Addresses of Drosophila researchers are copyrighted (GSA) material and only provided for official business of the Fly Board.<br />
<br />
===Map conversion tables===<br />
====Cytological <=> Sequence (genome-cyto-seq.txt)====<br />
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [[FlyBase:Computed_cytological_data|section G.5.1.]] of the Reference manual.<br />
<br />
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.<br />
<br />
The columns in the file are:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|Cytogenetic map position as described by Bridges.<br />
|-<br />
|'''-'''<br />
|First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|'''-'''<br />
|Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Cytological <=> Genetic (cytotable.txt)====<br />
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.<br />
<br />
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.<br />
<br />
<br />
====Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)====<br />
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 6 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Cytogenetic map position'''<br />
|Cytogenetic map position.<br />
|-<br />
|'''Genetic map position'''<br />
|Genetic map position.<br />
|-<br />
|'''Sequence coordinates (release 6)'''<br />
|Sequence coordinates (release 6) for the interval.<br />
|-<br />
|'''R6 conversion notes'''<br />
|<br />
|-<br />
|}<br />
<br />
<br />
An html version of this file is also available - see the [http://{{flybaseorg}}/static_pages/docs/cytotable3.html Map Conversion Table] page.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_fb_*.tsv)====<br />
This is identical to the file listed under the genes section above.<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Downloads_Overview&diff=170215FlyBase:Downloads Overview2019-01-14T17:01:54Z<p>Sian: /* Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json) */</p>
<hr />
<div>==Introduction==<br />
<br />
The "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page]" (referred to herein as the "Precomputed files" page) lists data files generated from the current release of FlyBase and links to the [ftp://ftp.flybase.net/releases/current/ current FTP repository]. Data from the previous five releases can be found on the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=archivedata3.html&title=Archived%20Releases Archived data files for recent releases]" page (referred to herein as the "Archived data" page), as well as links to servers hosting older releases of FlyBase, and all the release notes and news archives from FB2006_01. If you are looking for old data and cannot find it on the "Archived data" page please follow a link to the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
===Known issues===<br />
<br />
Safari does not connect properly to the FlyBase FTP site. You should be able to download individual files using Safari but you will not be able to browse the FTP repository.<br />
<br />
==The FTP archive==<br />
<br />
The "Main Data Set" section of the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Precomputed files]" page provides links to FlyBase FTP repository. The "Chado database" link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:<br />
<br />
$ psql -h chado.flybase.org -U flybase flybase<br />
<br />
The version running on this service is identical to the current web site release.<br />
<br />
The "Drosophila Data" section contains links to other sections of the FTP repository. The data can be accessed either by the version of FlyBase (The "[ftp://ftp.flybase.net/releases/current/ Current FTP repository]") or for sequence data by the annotation release of a particular Drosophila species (see the "[ftp://ftp.flybase.net/genomes/ Genomes FTP archive]")<br />
<br />
==General information about the available files==<br />
<br />
===File names===<br />
The first part of a filename always describes the content of the file, for example the file fbgn_annotation_ID_fb_2008_10.tsv.gz maps the primary FlyBase identifiers to the annotation symbols used for genes.<br />
<br />
Many of the precomputed data filenames also contain a release or version number. In the example above "fb_2008_10" denotes version FB2008_10 of FlyBase. Sequence data files, such as dmel-all-CDS-r5.13.fasta.gz, denote the annotation release that the data relates to as '-r5.13'. The 'r5' indicates the data is taken from the release 5 of the sequence assembly and the '13' after the decimal point specifies the annotation release.<br />
<br />
The following notation is used for different file formats: <br />
<br />
:'''Tab separated files''' are indicated by the extension ''''.tsv''''<br />
:'''[http://www.geneontology.org/GO.format.shtml#oboflat OBO format files]''', which are used for the ontologies, are denoted ''''.obo''''<br />
:'''Plain text''' files are given the extension ''''.txt''''<br />
:Files containing nucleic acid or polypeptide sequence data in the '''FASTA''' format are listed as ''''.fasta''''<br />
:'''GFF''' files include the suffix ''''.gff''''<br />
:'''GTF''' files include the suffix ''''.gtf''''<br />
:'''XML''' data files are denoted ''''.xml''''<br />
<br />
Most of the files listed on the "Precomputed files" page and the "Archived data" page are compressed with the [http://www.gzip.org/ GNU gzip] program. These files end with the suffix '.gz'. The ontology files are compressed in the ZIP file format, as indicated by the suffix '.zip'.<br />
<br />
===Accessing files===<br />
Files can be downloaded either directly through the web interface, or by using an ftp client such as wget to obtain the file from the FTP repository. Please note that at present Safari fails to connect to the FTP repository correctly, so we recommend that you use another browser if you wish to access the files through the web interface. The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file. Archived copies of the files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve this file for the FB2008_05 release, type:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
or more specifically:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_fb_2008_05.tsv.gz<br />
<br />
<br />
===Opening compressed files===<br />
Microsoft and Apple include built-in ZIP support in later versions of their operating systems. These files can also be opened with the free program [http://www.7-zip.org/ 7-zip].<br />
<br />
On OS X or Unix a GZIP compressed file can be extracted with the gunzip command. On a Windows machine we suggest that you use the program [http://www.7-zip.org/ 7-zip] to open these files, because several people have reported problems using WinZip. You should be able to open and read the resulting file with any text editor. <br />
<br />
<br />
==Types of files available==<br />
<br />
===XML files===<br />
<br />
These files are generated from the PostgreSQL Chado database for each release of FlyBase. The Chado XML files contain all the information used to generate the report pages and reflect the organization of the data in the database. The DTDs for these XML files, listing the structure of the files, are posted in the chado-xml directory of the FTP repository for each release. For the latest versions of the DTDs please see:<br />
<br />
ftp://ftp.flybase.net/releases/current/chado-xml/<br />
<br />
The XML files can also be obtained directly from the "Precomputed files" page by clicking on the "download" link under the ChadoXML heading in the appropriate section. The Chado XML files are available for genes, alleles, stocks, transcripts, polypeptides, insertions, transgenic (recombinant) constructs, aberrations, balancers, clones, and references.<br />
<br />
===Ontology files===<br />
<br />
The [http://{{flybaseorg}}/static_pages/docs/refman/refman-G.html#G.2. controlled vocabularies] (aka ontologies) used by FlyBase are available under the Ontology Terms section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page. Each controlled vocabulary is described in detail in [[FlyBase:Controlled vocabularies used by FlyBase|section G.2]]. of the Reference Manual. The files are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and are designed to be used with the free [http://www.oboedit.org/ OBO-Edit] tool.<br />
<br />
Controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects. On the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page the frozen versions of the controlled vocabularies used for the current release of FlyBase are available, and there are also links to the current 'live' versions maintained by the [http://www.obofoundry.org/ Open Biomedical Ontology] group.<br />
<br />
Frozen versions of the controlled vocabularies used for previous releases of FlyBase are available on the "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" page, and in the following directories of the FTP repository:<br />
<br />
ftp://ftp.flybase.net/releases/<RELEASE_NUMBER>/precomputed_files/ontologies/<br />
<br />
For example see:<br />
<br />
ftp://ftp.flybase.net/releases/FB2008_03/precomputed_files/ontologies/<br />
<br />
===FASTA files===<br />
<br />
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:<br />
<br />
'''dmel-all-<data type>-r<release-number>.fasta.gz'''<br />
<br />
or<br />
<br />
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''<br />
<br />
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome. <br />
<br />
{| class= "wikitable"<br />
!Data Type <br />
!Content Description<br />
|-<br />
|'''aligned ''' <br />
|The region of genomic sequence that analysis features align to.<br />
|-<br />
|'''CDS''' <br />
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.<br />
|-<br />
|'''chromosome'''<br />
|The sequence of each chromosome arm.<br />
|-<br />
|'''clones''' <br />
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.<br />
|-<br />
|'''exon ''' <br />
|The sequence of each exon split up into individual FASTA records.<br />
|-<br />
|'''five_prime_UTR'''<br />
|The sequence of 5' untranslated regions.<br />
|-<br />
|'''gene''' <br />
|The sequence of the gene span.<br />
|-<br />
|'''gene_extended2000''' <br />
|The sequence of the gene span with 2000 base pairs added upstream and downstream.<br />
|-<br />
|'''intergenic'''<br />
|The sequence of chromosomal regions between genes that do not contain known gene models.<br />
|-<br />
|'''intron''' <br />
|The sequence of each intron split up into individual FASTA records.<br />
|-<br />
|'''miRNA''' <br />
|The sequence of transcripts that are typed as micro RNAs.<br />
|-<br />
|'''miscRNA''' <br />
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.<br />
|-<br />
|'''ncRNA''' <br />
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).<br />
|-<br />
|'''predicted''' <br />
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.<br />
|-<br />
|'''pseudogene''' <br />
|The sequence of transcripts that are typed as pseudogenes.<br />
|-<br />
|'''sequence_features''' <br />
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.<br />
|-<br />
|'''synteny'''<br />
|The sequence of syntenic regions between two species.<br />
|-<br />
|'''three_prime_UTR'''<br />
|The sequence of 3' untranslated regions.<br />
|-<br />
|'''transcript'''<br />
|The sequence of transcripts that are typed as messenger RNAs (mRNA).<br />
|-<br />
|'''translation''' <br />
|The resulting protein sequence from protein coding transcripts.<br />
|-<br />
|'''transposon'''<br />
|The sequence of transposable elements.<br />
|-<br />
|'''tRNA''' <br />
|The sequence of transcripts that are typed as transfer RNAs (tRNA).<br />
|}<br />
<br />
<br />
====FASTA header format====<br />
<br />
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format<br />
<br />
'''field_name=value;'''<br />
<br />
Multiple field values are separated by commas<br />
<br />
'''field_name=value1,value2;'''<br />
<br />
This table describes some of the field names found in our FASTA headers <br />
<br />
{|class = "wikitable"<br />
<br />
!Field Name<br />
!Description<br />
|-<br />
|'''type''' <br />
|The feature type of the FASTA sequence record.<br />
|-<br />
|'''loc''' <br />
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.<br />
|-<br />
|'''ID''' <br />
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.<br />
|-<br />
|'''name'''<br />
|The name or symbol of the feature.<br />
|-<br />
|'''dbxref'''<br />
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.<br />
|-<br />
|'''MD5'''<br />
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.<br />
|-<br />
|'''length'''<br />
|The length of the sequence found in the FASTA record.<br />
|-<br />
|'''release'''<br />
|The release number denotes the annotation release which this FASTA record corresponds to.<br />
|-<br />
|'''species'''<br />
|The species abbreviation that this FASTA record corresponds to.<br />
|}<br />
<br />
<br />
===GFF files===<br />
<br />
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features. The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gff/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gff/<br />
<br />
For melanogaster, there are 3 GFF files distributed, they include:<br />
<br />
:'''dmel-all-r<release-number>.gff.gz'''<br />
::Contains all chromosome arms<br />
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''<br />
::Same as above except all match and match_part features have been removed<br />
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''<br />
::Contains only a single chromosome arm as identifed by the filename<br />
<br />
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues. <br />
<br />
===GTF files===<br />
<br />
The FlyBase GTF files follow the [http://mblab.wustl.edu/GTF22.html GTF v2.2] specification. The GTF files contain feature line definitions for gene models. The GTF are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gtf/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gtf/<br />
<br />
===Precomputed data text files===<br />
<br />
Precomputed data files that contain useful sets of data are generated for every release of FlyBase. For example, the file fbgn_NAseq_Uniprot_fb_2008_10.tsv.gz contains the mapping between valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] and the corresponding nucleic acid and protein accession numbers used by DDBJ/EMBL/GenBank and UniprotKB/Swiss-Prot/TrEMBL. These files can be found under the "Other" heading of each section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" and "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" pages, and are also available under the precomputed_files directory of each FlyBase release in the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.<br />
<br />
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.<br />
<br />
Each precomputed data file available for download on the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page contains the complete data set for the FlyBase release. Please note, if you are only looking for information on a defined subset of genes, or other FlyBase data type, you can query the current set of precomputed data files through the [http://{{flybaseorg}}/batchdownload Batch Download] tool to obtain the data you require. This approach is described in more detail in [https://wiki.flybase.org/wiki/FlyBase:Batch_Download this] help document.<br />
<br />
==Contents of the precomputed data text files listed by section==<br />
<br />
===Main data set===<br />
<br />
====Postgres Chado database dump====<br />
=====Chado database (ftp://ftp.flybase.net/releases/current/psql)=====<br />
The entire SQL Chado database is available for download. Follow the "README" directions herein.<br />
<br />
====Drosophila data====<br />
=====Current FTP repository (ftp://ftp.flybase.net/releases/current/)=====<br />
All files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Current Chado-XML repository (ftp://ftp.flybase.net/releases/current/chado-xml)=====<br />
All Chado XML files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Genomes FTP archive (ftp://ftp.flybase.net/genomes/)=====<br />
All FlyBase genome and genome annotation files are available for various Drosophila species. Formats include Chado XML, DNA, FASTA, GFF and GTF. Files from both the current release and previous FlyBase releases are offered. For release FB2018_05 and earlier, data is available for each of the original 12 sequenced Drosophila species. From release FB2018_06 onward, data is available only for D. melanogaster, D. simulans, D. ananassae, D. pseudoobscura and D. virilis.<br />
<br />
===Synonyms===<br />
<br />
====FlyBase Synonyms (fb_synonym_*.tsv)====<br />
The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).<br />
<br />
The file includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
* genes from drosophilid species and genes from non-drosophilids that have been introduced into transgenic flies<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''primary_FBid''' <br />
|Primary FlyBase identifier for the object.<br />
|-<br />
|'''organism_abbreviation''' <br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin.<br />
|-<br />
|'''current_symbol'''<br />
|Current symbol used in FlyBase for the object.<br />
|-<br />
|'''current_fullname''' <br />
|Current full name used in FlyBase for the object.<br />
|-<br />
|'''fullname_synonym(s)''' <br />
|Non-current full name(s) associated with the object (comma separated values).<br />
|-<br />
|'''symbol_synonym(s)'''<br />
|Non-current symbol(s) associated with the object (comma separated values).<br />
|-<br />
|}<br />
<br />
===Genes===<br />
<br />
====Genes data (Chado XML)====<br />
<br />
====Genetic interaction table (gene_genetic_interactions_*.tsv)====<br />
The file reports the summary of gene-level genetic interactions in FlyBase. This data is computed from the allele-level genetic interaction data captured by FlyBase curators.<br />
<br />
The file includes information for Dmel genes only.<br />
<br />
Interactions involving any of the following kinds of allele are considered when the gene-level genetic interaction data is computed:<br />
<br />
* classical mutations<br />
* alleles carried on transgenic constructs<br />
* loss-of-function mutations<br />
* gain-of-function mutations<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Starting_gene(s)_symbol''' <br />
|Current FlyBase symbol of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Starting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Interacting_gene(s)_symbol'''<br />
|Current FlyBase symbol of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interacting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interaction_type''' <br />
|Type of interaction observed, either 'suppressible' or 'enhanceable'.<br />
|-<br />
|'''Publication_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if the same genetic interaction has been reported in multiple references, multiple rows will exist for that genetic interaction in the file.<br />
<br />
* 'suppressible' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are suppressed by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
* 'enhanceable' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are enhanced by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
''e.g.''<br />
<br />
Pten&emsp;FBgn0026379&emsp;Akt1&emsp;FBgn0010379&emsp;suppressible&emsp;FBrf0127089<br />
<br />
indicates that phenotype(s) caused by a mutation of Pten are suppressed by a mutation of Akt1.<br />
<br />
* For cases where multiple genes are simultaneously mutated in either (or both) the starting and interacting genotype, then the genes involved are separated by a '|' in the relevant columns. In this case, the order of the list of symbols and of the list of ids in columns 1 and 2, or in columns 3 and 4 respectively are the same, so that the FBgn corresponding to the symbol for each gene can easily be identified.<br />
<br />
''e.g.''<br />
<br />
robo1|sli&emsp;FBgn0005631|FBgn0264089&emsp;RhoGAP93B&emsp;FBgn0038853&emsp;enhanceable&emsp;FBrf0191476<br />
<br />
indicates that:<br />
* phenotype(s) caused by a robo1, sli double mutant combination are enhanced by a mutation of RhoGAP93B.<br />
* FBgn0005631 corresponds to robo1, FBgn0264089 corresponds to sli<br />
<br />
<br />
<br />
====RNA-Seq RPKM values (gene_rpkm_report_fb_*.tsv.gz)====<br />
This file reports gene expression values based on RNA-Seq experiments, calculated as reads per kilobase per million reads (RPKM). RPKM values are calculated only for the unique exonic regions of the gene (excluding segments that overlap other genes), except for genes derived from dicistronic/polycistronic transcripts, in which case all exon regions are used in the RPKM expression calculation.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Release_ID'''<br />
|The D. melanogaster annotation set version from which the gene model used in the analysis derives.<br />
|-<br />
|'''FBgn#'''<br />
|The unique FlyBase gene ID for this gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|The official FlyBase symbol for this gene.<br />
|-<br />
|'''Parent_library_FBlc#'''<br />
|The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''Parent_library_name'''<br />
|The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''RNASource_FBlc#'''<br />
|The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RNASource_name'''<br />
|The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RPKM_value'''<br />
|The RPKM expression value for the gene in the specified RNA-Seq experiment.<br />
|-<br />
|'''Bin_value'''<br />
|The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression).<br />
|-<br />
|'''Unique_exon_base_count'''<br />
|The number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts.<br />
|-<br />
|'''Total_exon_base_count'''<br />
|The number of bases in all exons of this gene.<br />
|-<br />
|'''Count_used'''<br />
|Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Physical interaction table (physical_interactions_fb_*.tsv.gz)====<br />
This file reports unique gene pairs with curated support for some type of physical interaction. The file does not currently distinguish between genes that are involved in protein-protein or RNA-protein interactions (or both).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_FBgn1'''<br />
|The unique FlyBase gene ID for the first gene of the interacting pair.<br />
|-<br />
|'''gene_symbol1'''<br />
|The official FlyBase symbol for the first gene of the interacting pair.<br />
|-<br />
|'''gene_FBgn2'''<br />
|The unique FlyBase gene ID for the second gene of the interacting pair.<br />
|-<br />
|'''gene_symbol2'''<br />
|The official FlyBase symbol for the second gene of the interacting pair.<br />
|-<br />
|'''FBrf(s)'''<br />
|The unique FlyBase IDs for the publications supporting this interaction.<br />
|-<br />
|'''FBig_id'''<br />
|The unique FlyBase ID for this pairwise interaction.<br />
|-<br />
|'''#_reported_interactions'''<br />
|The number of distinct experiments in support of this interaction.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction MITAB file (physical_interactions_mitab_fb_*.tsv.gz)====<br />
This file reports each individual experiment curated by FlyBase that supports a physical interaction between two gene products. There can be multiple experiments (multiple rows in the file) between products of the same gene pair. Interaction molecule types currently curated are protein-protein, protein-RNA or RNA-RNA. <br />
<br />
This file is in PSI-MI TAB format, a tab-delimited format developed by the HUPO Proteomics Standards Initiative (PSI) Molecular Interactions (MI) working group to facilitate interactomics data comparison and exchange. Details on the general MITAB format can be found [https://psicquic.github.io/MITAB27Format.html here]. The file makes use of the Molecular Interactions ontology which can be searched or browsed [https://www.ebi.ac.uk/ols/ontologies/mi here]. Fields are filled with “-” if values are missing or not relevant.<br />
<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading<br />
!General format <br />
!FlyBase example<br />
!Content description<br />
|-<br />
|'''1'''<br />
|'''ID(s) Interactor A'''<br />
|database:identifier<br />
|flybase:FBgn0002121<br />
|The unique Flybase identifier for the first gene of the interacting pair.<br />
|-<br />
|'''2'''<br />
|'''ID(s) Interactor B'''<br />
|”<br />
|”<br />
|The unique Flybase identifier for the second gene of the interacting pair.<br />
|-<br />
|'''3'''<br />
|'''Alt ID(s) Interactor A'''<br />
|database:identifier<br />
|<nowiki>flybase:CG2671|entrez gene/locuslink:33156</nowiki><br />
|<nowiki>The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|”.</nowiki><br />
|-<br />
|'''4'''<br />
|'''Alt ID(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''5'''<br />
|'''Alias(es) Interactor A'''<br />
|database:name(alias type)<br />
|flybase:l(2)gl(gene name)<br />
|The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.<br />
|-<br />
|'''6'''<br />
|'''Alias(es) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''7'''<br />
|'''Interaction Detection Method(s)'''<br />
|ontology:identifier(method name)<br />
|psi-mi:"MI:0006"(anti bait coimmunoprecipitation)<br />
|The assay used to detect the interaction, taken from the psi-mi ontology.<br />
|-<br />
|'''8'''<br />
|'''Publication 1st Author(s)'''<br />
|surname initial(s) (publication year)<br />
|Betschinger K. (2003)<br />
|The first author and year of the publication where the interaction is described.<br />
|-<br />
|'''9'''<br />
|'''Publication ID(s)'''<br />
|database:identifier<br />
|<nowiki>flybase:FBrf0157155|pubmed:12629552</nowiki><br />
|<nowiki>The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.</nowiki><br />
|-<br />
|'''10'''<br />
|'''Taxid Interactor A'''<br />
|taxid:identifier<br />
|taxid:7227("Drosophila melanogaster")<br />
|The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.<br />
|-<br />
|'''11'''<br />
|'''Taxid Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''12'''<br />
|'''Interaction Type(s)'''<br />
|ontology:identifier(interaction type)<br />
|psi-mi:"MI:0915"(physical association)<br />
|Taken from the psi-mi ontology. Most often “physical association” for FlyBase.<br />
|-<br />
|'''13'''<br />
|'''Source Database(s)'''<br />
|ontology:identifier(database name)<br />
|psi-mi:"MI:0478"(flybase)<br />
|All interactions are curated by FlyBase.<br />
|-<br />
|'''14'''<br />
|'''Interaction Identifier(s)'''<br />
|database:identifier<br />
|flybase:FBrf0157155-13.coIP.WB<br />
|The unique FlyBase identifier for this interaction.<br />
|-<br />
|'''15'''<br />
|'''Confidence Value(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''16'''<br />
|'''Expansion Method(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''17'''<br />
|'''Biological Role(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''18'''<br />
|'''Biological Role(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''19'''<br />
|'''Experimental Role(s) Interactor A'''<br />
|ontology:identifier(experimental role name)<br />
|psi-mi:"MI:0496"(bait)<br />
|The role played by the interactor in the experiment. Taken from the psi-mi ontology.<br />
|-<br />
|'''20'''<br />
|'''Experimental Role(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''21'''<br />
|'''Type(s) Interactor A'''<br />
|ontology:identifier(interactor type name)<br />
|psi-mi:"MI:0326"(protein)<br />
|The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.<br />
|-<br />
|'''22'''<br />
|'''Type(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''23'''<br />
|'''Xref(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''24'''<br />
|'''Xref(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''25'''<br />
|'''Interaction Xref(s)'''<br />
|database:identifier<br />
|flybase:FBig0000000103<br />
|<nowiki>Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.</nowiki><br />
|-<br />
|'''26'''<br />
|'''Annotation(s) Interactor A'''<br />
|topic:text<br />
|isoform-comment:a isoform<br />
|Information on whether the interaction is specific to a particular interactor isoform.<br />
|-<br />
|'''27'''<br />
|'''Annotation(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''28'''<br />
|'''Interaction Annotation(s)'''<br />
|topic:text<br />
|molecular source:Source was cell extract of S2 cell line; bait produced from endogenous gene; prey produced from endogenous gene.|comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.<br />
|Describes the source(s) of the interaction participants and includes free text comments about the interaction.<br />
|-<br />
|'''29'''<br />
|'''Host Organism(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''30'''<br />
|'''Interaction Parameters'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''31'''<br />
|'''Creation Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''32'''<br />
|'''Update Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''33'''<br />
|'''Checksum Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''34'''<br />
|'''Checksum Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''35'''<br />
|'''Interaction Checksum'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''36'''<br />
|'''Negative'''<br />
|<br />
|FALSE<br />
|All interactions in FlyBase are positive.<br />
|-<br />
|'''37'''<br />
|'''Feature(s) Interactor A'''<br />
|feature_type:range(text)<br />
|sufficient binding region:aa 1-58(N-terminal region)<br />
|Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.<br />
|-<br />
|'''38'''<br />
|'''Feature(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''39'''<br />
|'''Stoichiometry Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''40'''<br />
|'''Stoichiometry Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''41'''<br />
|'''Identification Method(s) Participant A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''42'''<br />
|'''Identification Method(s) Participant B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|}<br />
<br />
<br />
====Functional complementation table (gene_functional_complementation_*.tsv)====<br />
<br />
This file reports when functional complementation of Dmel genes by non-Dmel orthologs has been observed. This data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature. The file contains a list of gene Dmel - to - non-Dmel-ortholog gene pairs where a transgenic construct/mutant allele of the non-Dmel ortholog has been shown to at least partially suppress mutant phenotype(s) of an allele of the Dmel gene.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''Dmel gene (symbol)'''<br />
|Current FlyBase symbol of Dmel gene.<br />
|-<br />
|'''2'''<br />
|'''Dmel gene (FBgn)'''<br />
|Current FlyBase identifier (FBgn#) of Dmel gene in column 1.<br />
|-<br />
|'''3'''<br />
|'''Functionally complementing ortholog (symbol)'''<br />
|Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''4'''<br />
|'''Functionally complementing ortholog (FBgn#)'''<br />
|Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''5'''<br />
|'''Supporting_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if multiple references support the same functional complementation statement, multiple rows will exist for that statement in the file.<br />
<br />
<br />
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====<br />
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, UniProtKB/SwissProt/TrEMBL protein accessions, NCBI Entrez gene IDs and NCBI RefSeq transcript and protein accessions associated with FlyBase genes.<br />
<br />
The file includes:<br />
* nuclear genes with sequence accession numbers<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes without sequence accession numbers<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''2'''<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''3'''<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''4'''<br />
|'''nucleotide_accession'''<br />
|EMBL/GenBank/DDBJ nucleotide accession associated with the gene.<br />
|-<br />
|'''5'''<br />
|'''na_based_protein_accession'''<br />
|EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column<br />
|-<br />
|'''6'''<br />
|'''UniprotKB/Swiss-Prot/TrEMBL_accession'''<br />
|UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.<br />
|-<br />
|'''7'''<br />
|'''EntrezGene_ID'''<br />
|NCBI Entrez ID associated with the gene.<br />
|-<br />
|'''8'''<br />
|'''RefSeq_transcripts'''<br />
|NCBI RefSeq transcript accession associated with the gene.<br />
|-<br />
|'''9'''<br />
|'''RefSeq_proteins'''<br />
|NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.<br />
<br />
* A single row contains '''only''' information about an EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession '''or''' an NCBI Entrez gene ID '''or''' an NCBI RefSeq transcript accession.<br />
<br />
* For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 4 ('nucleotide_accession'). If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 4, this protein accession is listed in column 5 ('na_based_protein_accession'). In this case, columns 6, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 6 ('UniprotKB/Swiss-Prot/TrEMBL_accession'). In this case, columns 4, 5, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI Entrez gene, an ID associated with the gene is listed in column 7 ('EntrezGene_ID'). In this case, columns 4, 5, 6, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI RefSeq accession, a transcript accession associated with the gene is listed in column 8 ('RefSeq_transcripts'). If there is also an NCBI RefSeq protein accession associated with that gene '''and''' with the transcript accession in column 8, this protein accession is listed in column 9 ('RefSeq_proteins'). In this case, columns 4, 5, 6 and 7 are always empty.<br />
<br />
<br />
<br />
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====<br />
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''secondary_FBgn#(s)'''<br />
|Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).<br />
|-<br />
|'''annotation_ID'''<br />
|Current annotation identifier associated with the gene.<br />
|-<br />
|'''secondary_annotation_ID(s)'''<br />
|Secondary annotation identifier(s) associated with the gene (comma separated values).<br />
|-<br />
|}<br />
Notes:<br />
<br />
* If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702). <br />
<br />
<br />
<br />
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====<br />
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.<br />
<br />
The file includes:<br />
* non-melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* ''D. melanogaster'' genes<br />
* non-melanogaster genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''gene_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GLEANR_ID'''<br />
|GLEANR identifier assigned by the AAA Consortium.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====<br />
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.<br />
<br />
The file includes:<br />
* genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FlyBase_FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FlyBase_FBtr'''<br />
|Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.<br />
|-<br />
|'''FlyBase_FBpp'''<br />
|Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript and the polypeptide it encodes (if relevant). Thus if a gene encodes multiple isoforms, multiple rows with exist for that gene in the file.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====<br />
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.<br />
<br />
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.<br />
<br />
The file includes the following '''Dmel''' genes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
Notes:<br />
<br />
* Each line of the file '''can contain many''' tab separated columns:<br />
<br />
* '''The first column of a line''' contains the valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] of a gene.<br />
* '''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====<br />
The file is generated from the location of Affy2 oligos exactly as [[FlyBase:FilesOverview#5.2.6|described for Affy1 oligos]] above.<br />
<br />
<br />
<br />
====Genes GO data (gene_association.fb)====<br />
The file contains the [http://www.geneontology.org/ Gene Ontology] (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.<br />
<br />
The file includes the following Dmel genes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
The columns of the file are described in [[FlyBase:Gene Ontology (GO) Annotation|section G.3.1.]] of the Reference manual.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_*.tsv)====<br />
The file reports available localization information for FlyBase genes.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''current_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBid'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''recombination_loc'''<br />
|recombination map location.<br />
|-<br />
|'''cytogenetic_loc'''<br />
|cytogenetic location.<br />
|-<br />
|'''sequence_loc'''<br />
|genomic location.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Automated gene summaries (automated_gene_summaries.tsv)====<br />
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|FlyBase ID. The Valid FlyBase identifier number for the gene.<br />
|-<br />
|'''-'''<br />
|The gene summary as a string of plain text.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Gene Snapshots (gene_snapshots_*.tsv)====<br />
The file contains in plain text the gene snapshot information visible on gene report pages.<br />
<br />
It includes only Dmel protein coding genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier number for the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase symbol of the gene.<br />
|-<br />
|'''GeneName'''<br />
|Current FlyBase name of the gene.<br />
|-<br />
|'''datestamp'''<br />
|Date on which the information was last reviewed.<br />
|-<br />
|'''gene_snapshot_text'''<br />
|Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Unique protein isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their unique protein isoforms.<br />
<br />
The file includes:<br />
* melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* melanogaster genes not located to the sequence<br />
* non-melanogaster genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FB_gene_symbol'''<br />
|Current FlyBase gene symbol of the gene.<br />
|-<br />
|'''representative_protein'''<br />
|Current FlyBase protein symbol of the representative protein isoform.<br />
|-<br />
|'''identical_protein(s)'''<br />
|Current FlyBase protein symbol(s) of identical protein isoforms.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNA genes (TSV) (ncRNA_genes_fb_*.tsv.gz)====<br />
This file reports all genes encoding ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in TSV format. Pseudogenes are excluded.<br />
<br />
Columns are:<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''accession_id'''<br />
|INSDC accession ID.<br />
|-<br />
|'''FB_gene_ID'''<br />
|Current FlyBase gene identifier (FBgn#).<br />
|-<br />
|'''species_FB_annotation_ID(locus_tag)'''<br />
|Current FlyBase annotation ID, in the form "<species abbreviation>_<annotation_ID>", which equates to the 'locus tag' field in INSDC records.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Gene groups===<br />
====Gene group data (gene_group_data_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with their hierarchical relationships (where relevant) and member genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''Parent_FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Parent_FB_group_symbol'''<br />
|Current FlyBase symbol of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Group_member_FB_gene_id'''<br />
|Current FlyBase identifier (FBgn##) of member gene (if terminal group).<br />
|-<br />
|'''Group_member_FB_gene_symbol'''<br />
|Current FlyBase symbol of member gene (if terminal group).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Where groups are arranged into hierarchies:<br />
** the member genes are only associated with the terminal subgroups,<br />
** the immediate parent of any subgroup is identified in the ‘Parent_FB_group_id' and 'Parent_FB_group_symbol' columns.<br />
<br />
* Separate lines are used for each member gene, meaning that each terminal group is listed multiple times (equal to the number of member genes).<br />
<br />
<br />
<br />
====Gene groups with HGNC IDs (gene_groups_HGNC_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with the corresponding HGNC 'gene family' ID (where relevant).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''HGNC_family_ID'''<br />
|HGNC ID of equivalent human 'gene family'.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* The absence of an HGNC_family_ID entry indicates there is no equivalent HGNC gene family for that FlyBase gene group.<br />
<br />
* Because of different sub-group structures (etc), a single HGNC family may be associated with multiple FlyBase gene groups.<br />
<br />
* Similarly, a single FlyBase gene group may be associated with multiple HGNC gene families - these are shown on separate lines.<br />
<br />
<br />
<br />
===Alleles and Stocks===<br />
====Allele data (Chado XML)====<br />
<br />
====Stock data (Chado XML)====<br />
<br />
====Stock data (stocks_*.tsv.gz)====<br />
This file reports genetic components and related information about Stocks in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
!Example<br />
|-<br />
|'''FBst'''<br />
|The unique identifier assigned to this stock by FlyBase.<br />
|FBst0000002<br />
|-<br />
|'''collection_short_name'''<br />
|A short name for the stock collection that holds the stock.<br />
|Bloomington<br />
|-<br />
|'''stock_type_cv'''<br />
|The controlled vocabulary term and unique identifier that describe the state of the stock.<br />
|living stock ; FBsv:0000002<br />
|-<br />
|'''species'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of the stock.<br />
|Dmel<br />
|-<br />
|'''FB_genotype'''<br />
|Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.<br />
|w[*]; betaTub60D[2] Kr[If-1]/CyO<br />
|-<br />
|'''description'''<br />
|Genetic components of the stock as provided to FlyBase by the collection that holds the stock.<br />
|FlyTrap: ZCL1796 III<br />
|-<br />
|'''stock_number'''<br />
|The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.<br />
|110818<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genetic interactions (allele_genetic_interactions_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''interaction'''<br />
|Interaction information associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single interaction from a single reference. Thus if multiple genetic interactions have been reported for a given allele, or if multiple references report the same interaction for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Phenotypic data (allele_phenotypic_data_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''phenotype'''<br />
|Phenotypic data associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes: <br />
<br />
* Each row contains information about a single phenotype from a single reference. Thus if multiple phenotypes have been reported for a given allele, or if multiple references report the same phenotype for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Alleles <=> Genes (fbal_to_fbgn_fb_*.tsv)====<br />
This file reports the relationship between gene identifiers and the identifiers used for alleles of these genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''AlleleID'''<br />
|Current FlyBase identifier (FBal#) of the allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current symbol of the allele.<br />
|-<br />
|'''GeneID'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Orthologs===<br />
<br />
====Drosophila Orthologs (dmel_orthologs_in_drosophila_species_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their orthologs in other sequenced Drosophila genomes, as determined by OrthoDB. (The version of OrthoDB currently being used is shown in the 'Orthologs' -> 'Orthologs (via OrthoDB)' section of a Gene Report.)<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Ortholog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_Arm/Scaffold'''<br />
|Arm upon which the non-melanogaster orthologous gene is localized.<br />
|-<br />
|'''Ortholog_Location'''<br />
|Location of non-melanogaster orthologous gene on the arm.<br />
|-<br />
|'''Ortholog_Strand'''<br />
|Strand of non-melanogaster orthologous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''OrthoDB_Group_ID'''<br />
|OrthoDB orthology group ID to which the pair-wise association belongs.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association beween a ''D. melanogaster'' gene and a non-melanogaster ortholog. Thus, multiple rows exist for each ''D. melanogaster'' gene in the file.<br />
<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dmel_gene_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Dmel_gene_symbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Human_gene_HGNC_ID'''<br />
|HGNC ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_OMIM_ID'''<br />
|OMIM ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_symbol'''<br />
|HGNC gene symbol of orthologous human gene.<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|'''OMIM_Phenotype_IDs'''<br />
|OMIM Phenotype ID of orthologous human gene (comma separated values).<br />
|-<br />
|'''OMIM_Phenotype_IDs[name]'''<br />
|OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets). Multiple phenotype[name] entries are separated by a comma.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Human disease===<br />
<br />
====Human disease model data (allele_human_disease_model_data_fb_*.tsv.gz)====<br />
This file reports all experimental-based disease model annotations, associated with alleles, that have been curated for ''D. melanogaster''. 'Alleles' encompasses both classical alleles and transgenic alleles; the latter may relate to transgenic constructs of ''D. melanogaster'' genes or non-''D. melanogaster'' genes, often human genes. These are the data reported in the "Human Disease Model Data" -> "Disease Ontology" section of the Allele Report, which are repeated in the "Human Disease Model Data" -> "Alleles Reported to Model Human Disease (Disease Ontology)" section of the Gene Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBal_ID'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current FlyBase symbol of allele.<br />
|-<br />
|'''DOID_qualifier'''<br />
|Annotation qualifier - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.<br />
|-<br />
|'''DOID_term'''<br />
|Disease Ontology term.<br />
|-<br />
|'''DOID_ID'''<br />
|Disease Ontology ID.<br />
|-<br />
|'''Evidence/interacting_alleles'''<br />
|Evidence code, with interacting allele(s) where appropriate. Evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma.<br />
|-<br />
|'''Reference_FBid'''<br />
|Current FlyBase identifier (FBrf#) of the publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
This is identical to the file of the same name listed under the 'Orthologs' section above. <br />
<br />
<br />
<br />
===Nomenclature===<br />
<br />
====Species abbreviation list (species-ab.gz)====<br />
<br />
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.<br />
<br />
There are 8 columns of data in the file, each separated by " | ".<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Internal_id'''<br />
|The Primary [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the organism.<br />
|-<br />
|'''Taxgroup'''<br />
|A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".<br />
|-<br />
|'''Abbreviation'''<br />
|The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.<br />
|-<br />
|'''Genus'''<br />
|The genus name of the organism.<br />
|-<br />
|'''Species name'''<br />
|The species name of the organism.<br />
|-<br />
|'''Common name'''<br />
|The common name of the organism. This column may be blank.<br />
|-<br />
|'''Comment'''<br />
|A free text field for additional comments. This column may be blank.<br />
|-<br />
|'''Ncbi-taxon-id'''<br />
|The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.<br />
|-<br />
|}<br />
<br />
An html version of this file is also available - see the [[FlyBase:Abbreviations|Species Abbreviations]] page.<br />
<br />
<br />
<br />
===Ontology Terms===<br />
====Frozen files used for this release of FlyBase====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
* FBdv: fly_development<br />
* FBcv: flybase controlled vocabulary<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
====Current 'Live' Files====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_anatomy.obo' version''<br />
* FBdv: fly_development<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_development.obo' version''<br />
* FBcv: flybase controlled vocabulary<br />
''Note: link points to the ontology version fbcv-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'flybase_controlled_vocabulary.obo' version''<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
===Genomes: Annotation and Sequence===<br />
====All Sequenced Drosophila Species====<br />
<br />
Links are available to the following FTP repositories:<br />
<br />
* Current FTP repository<br />
* Current FastA repository<br />
* Current GFF repository<br />
<br />
* FTP archive (previous releases)<br />
<br />
* Current list of individual FASTA files<br />
* Current list of individual GFF files<br />
<br />
For release FB2018_06 onward, the above links are available for the following sequenced Drosophila species:<br />
<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila melanogaster<br />
|Dmel<br />
|-<br />
|Drosophila ananassae<br />
|Dana<br />
|-<br />
|Drosophila pseudoobscura pseudoobscura<br />
|Dpse<br />
|-<br />
|Drosophila simulans<br />
|Dsim<br />
|-<br />
|Drosophila virilis<br />
|Dvir<br />
|-<br />
|}<br />
<br />
<br />
For earlier archived releases, the above links are also available for these additional species (other members of the original 12 sequenced Drosophila species):<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila erecta<br />
|Dere<br />
|-<br />
|Drosophila grimshawi<br />
|Dgri<br />
|-<br />
|Drosophila mojavensis<br />
|Dmoj<br />
|-<br />
|Drosophila persimilis<br />
|Dper<br />
|-<br />
|Drosophila sechellia<br />
|Dsec<br />
|-<br />
|Drosophila willistoni<br />
|Dwil<br />
|-<br />
|Drosophila yakuba<br />
|Dyak<br />
|-<br />
|}<br />
<br />
===Transcripts and Polypeptides===<br />
<br />
====Transcript data (Chado XML)====<br />
<br />
====Polypeptide data (Chado XML)====<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Transposons, Transgenic Constructs, and Insertions===<br />
<br />
====Insertions (Chado XML)====<br />
====Transgenic Constructs (Chado XML)====<br />
<br />
<br />
====Transgenic construct maps (construct_maps.zip)====<br />
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the respective recombinant construct or transgenic transposon.<br />
<br />
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.<br />
<br />
====Map data for insertions (insertion_mapping_*.tsv)====<br />
The insertion mapping table reports available localization information for '''Dmel''' insertions.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''insertion_symbol'''<br />
|Current symbol of insertion.<br />
|-<br />
|'''FBti#'''<br />
|Current FlyBase identifier (FBti#) of insertion<br />
.<br />
|-<br />
|'''genomic_location'''<br />
|Genomic location of insertion.<br />
|-<br />
|'''range'''<br />
|Range (t/f) indicates whether genomic location is range or single base.<br />
|-<br />
|'''orientation'''<br />
|Orientation (1/0) indicates orientation of insertion on chromosome.<br />
|-<br />
|'''estimated_cytogenetic_location'''<br />
|Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.<br />
|-<br />
|'''observed_cytogenetic_location'''<br />
|Observed cytogenetic location reported in the literature.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====<br />
This is a file of 'canonical' sequences of the transposable elements from Drosophila maintained by M. Ashburner.<br />
<br />
The first section of the file outlines the history and revisions to the file and also lists the current set of elements, their size and whether the subsequent sequence data is complete.<br />
<br />
The second section of the file, which is separated from the first by a line of "_" characters contains the sequence data of all the elements in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL format]. The record for each element starts with a line prefixed by "ID" and ends with a line containing "//".<br />
<br />
====Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json)====<br />
This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the Bloomington Drosophila Stock Center, in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format [http://flybase.org/GAL4/freq_used_drivers.tsv here].<br />
<br />
===Aberrations===<br />
====Aberration data (Chado XML)====<br />
====Balancer data (Chado XML)====<br />
<br />
===Large dataset metadata===<br />
====Dataset metadata members (dataset_metadata_fb_*.tsv.gz)====<br />
This file lists all features that are associated with a dataset/collection (e.g., genes, cDNA clones, TF_binding_sites, Affymetrix probes).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dataset_Metadata_ID'''<br />
|The unique FlyBase ID for the dataset.<br />
|-<br />
|'''Dataset_Metadata_Name'''<br />
|The official FlyBase symbol for the dataset.<br />
|-<br />
|'''Item_ID'''<br />
|The unique FlyBase ID for the feature associated with this dataset.<br />
|-<br />
|'''Item_Name'''<br />
|The official FlyBase symbol for the feature associated with this dataset.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Clones===<br />
<br />
====Clone data (Chado XML)====<br />
<br />
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====<br />
The file reports basic cDNA clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of cDNA clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''dataset_metadata_name'''<br />
|Name of dataset associated with clone.<br />
|-<br />
|'''cDNA_accession(s)'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|'''EST_accession(s)'''<br />
|EMBL/GenBank/DDBJ EST accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====<br />
<br />
The file reports basic genomic clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of genomic clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''accession'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===References===<br />
====Combined reference data (Chado XML)====<br />
====FlyBase FBrf <=> PubMed ID <=> PMCID <=> DOI (fbrf_pmid_pmcid_doi_fb_*.tsv.gz)====<br />
<br />
This file lists all publications in the FlyBase bibliography that have a PubMed ID. Additional identifiers are listed as applicable.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBrf'''<br />
|The unique FlyBase ID for this publication.<br />
|-<br />
|'''PMID'''<br />
|The unique PubMed ID for this publication.<br />
|-<br />
|'''PMCID'''<br />
|The unique PubMed Central ID for this publication, if applicable.<br />
|-<br />
|'''DOI'''<br />
|The digital object identifier assigned to the publication.<br />
|-<br />
|'''pub_type'''<br />
|The publication type (for example, paper, review, erratum, abstract, book, etc.)<br />
|-<br />
|'''miniref'''<br />
|A short citation listing the first author, year of publication, journal, volume, issue and page numbers.<br />
|-<br />
|'''pmid_added'''<br />
|The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Drosophila researchers===<br />
Addresses of Drosophila researchers are copyrighted (GSA) material and only provided for official business of the Fly Board.<br />
<br />
===Map conversion tables===<br />
====Cytological <=> Sequence (genome-cyto-seq.txt)====<br />
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [[FlyBase:Computed_cytological_data|section G.5.1.]] of the Reference manual.<br />
<br />
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.<br />
<br />
The columns in the file are:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|Cytogenetic map position as described by Bridges.<br />
|-<br />
|'''-'''<br />
|First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|'''-'''<br />
|Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Cytological <=> Genetic (cytotable.txt)====<br />
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.<br />
<br />
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.<br />
<br />
<br />
====Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)====<br />
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 6 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Cytogenetic map position'''<br />
|Cytogenetic map position.<br />
|-<br />
|'''Genetic map position'''<br />
|Genetic map position.<br />
|-<br />
|'''Sequence coordinates (release 6)'''<br />
|Sequence coordinates (release 6) for the interval.<br />
|-<br />
|'''R6 conversion notes'''<br />
|<br />
|-<br />
|}<br />
<br />
<br />
An html version of this file is also available - see the [http://{{flybaseorg}}/static_pages/docs/cytotable3.html Map Conversion Table] page.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_fb_*.tsv)====<br />
This is identical to the file listed under the genes section above.<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Downloads_Overview&diff=170214FlyBase:Downloads Overview2019-01-14T17:00:21Z<p>Sian: /* Transposons, Transgenic Constructs, and Insertions */</p>
<hr />
<div>==Introduction==<br />
<br />
The "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Current Release page]" (referred to herein as the "Precomputed files" page) lists data files generated from the current release of FlyBase and links to the [ftp://ftp.flybase.net/releases/current/ current FTP repository]. Data from the previous five releases can be found on the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=archivedata3.html&title=Archived%20Releases Archived data files for recent releases]" page (referred to herein as the "Archived data" page), as well as links to servers hosting older releases of FlyBase, and all the release notes and news archives from FB2006_01. If you are looking for old data and cannot find it on the "Archived data" page please follow a link to the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
===Known issues===<br />
<br />
Safari does not connect properly to the FlyBase FTP site. You should be able to download individual files using Safari but you will not be able to browse the FTP repository.<br />
<br />
==The FTP archive==<br />
<br />
The "Main Data Set" section of the "[http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=bulkdata7.html&title=Current%20Release Precomputed files]" page provides links to FlyBase FTP repository. The "Chado database" link leads to the psql directory of the current FTP repository where you can obtain a dump of the PostgreSQL Chado database. If you have a PostgreSQL client application installed and would like to access the latest FlyBase release without installing the database you can connect to the FlyBase public read only Chado database as:<br />
<br />
$ psql -h chado.flybase.org -U flybase flybase<br />
<br />
The version running on this service is identical to the current web site release.<br />
<br />
The "Drosophila Data" section contains links to other sections of the FTP repository. The data can be accessed either by the version of FlyBase (The "[ftp://ftp.flybase.net/releases/current/ Current FTP repository]") or for sequence data by the annotation release of a particular Drosophila species (see the "[ftp://ftp.flybase.net/genomes/ Genomes FTP archive]")<br />
<br />
==General information about the available files==<br />
<br />
===File names===<br />
The first part of a filename always describes the content of the file, for example the file fbgn_annotation_ID_fb_2008_10.tsv.gz maps the primary FlyBase identifiers to the annotation symbols used for genes.<br />
<br />
Many of the precomputed data filenames also contain a release or version number. In the example above "fb_2008_10" denotes version FB2008_10 of FlyBase. Sequence data files, such as dmel-all-CDS-r5.13.fasta.gz, denote the annotation release that the data relates to as '-r5.13'. The 'r5' indicates the data is taken from the release 5 of the sequence assembly and the '13' after the decimal point specifies the annotation release.<br />
<br />
The following notation is used for different file formats: <br />
<br />
:'''Tab separated files''' are indicated by the extension ''''.tsv''''<br />
:'''[http://www.geneontology.org/GO.format.shtml#oboflat OBO format files]''', which are used for the ontologies, are denoted ''''.obo''''<br />
:'''Plain text''' files are given the extension ''''.txt''''<br />
:Files containing nucleic acid or polypeptide sequence data in the '''FASTA''' format are listed as ''''.fasta''''<br />
:'''GFF''' files include the suffix ''''.gff''''<br />
:'''GTF''' files include the suffix ''''.gtf''''<br />
:'''XML''' data files are denoted ''''.xml''''<br />
<br />
Most of the files listed on the "Precomputed files" page and the "Archived data" page are compressed with the [http://www.gzip.org/ GNU gzip] program. These files end with the suffix '.gz'. The ontology files are compressed in the ZIP file format, as indicated by the suffix '.zip'.<br />
<br />
===Accessing files===<br />
Files can be downloaded either directly through the web interface, or by using an ftp client such as wget to obtain the file from the FTP repository. Please note that at present Safari fails to connect to the FTP repository correctly, so we recommend that you use another browser if you wish to access the files through the web interface. The ftp client wget accepts wild card patterns which means you can use a query of the following kind to obtain the latest file without having to specify the FlyBase release number:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/current/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
The /releases/current/ path will always point to latest FlyBase release and this directory will have only one copy of the file. Archived copies of the files from previous releases can be obtained by including the FlyBase release in the path /releases/<RELEASE_NUMBER>/. For example to retrieve this file for the FB2008_05 release, type:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_*.tsv.gz<br />
<br />
or more specifically:<br />
<br />
$ wget ftp://ftp.flybase.net/releases/FB2008_05/precomputed_files/genes/fbgn_annotation_ID_fb_2008_05.tsv.gz<br />
<br />
<br />
===Opening compressed files===<br />
Microsoft and Apple include built-in ZIP support in later versions of their operating systems. These files can also be opened with the free program [http://www.7-zip.org/ 7-zip].<br />
<br />
On OS X or Unix a GZIP compressed file can be extracted with the gunzip command. On a Windows machine we suggest that you use the program [http://www.7-zip.org/ 7-zip] to open these files, because several people have reported problems using WinZip. You should be able to open and read the resulting file with any text editor. <br />
<br />
<br />
==Types of files available==<br />
<br />
===XML files===<br />
<br />
These files are generated from the PostgreSQL Chado database for each release of FlyBase. The Chado XML files contain all the information used to generate the report pages and reflect the organization of the data in the database. The DTDs for these XML files, listing the structure of the files, are posted in the chado-xml directory of the FTP repository for each release. For the latest versions of the DTDs please see:<br />
<br />
ftp://ftp.flybase.net/releases/current/chado-xml/<br />
<br />
The XML files can also be obtained directly from the "Precomputed files" page by clicking on the "download" link under the ChadoXML heading in the appropriate section. The Chado XML files are available for genes, alleles, stocks, transcripts, polypeptides, insertions, transgenic (recombinant) constructs, aberrations, balancers, clones, and references.<br />
<br />
===Ontology files===<br />
<br />
The [http://{{flybaseorg}}/static_pages/docs/refman/refman-G.html#G.2. controlled vocabularies] (aka ontologies) used by FlyBase are available under the Ontology Terms section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page. Each controlled vocabulary is described in detail in [[FlyBase:Controlled vocabularies used by FlyBase|section G.2]]. of the Reference Manual. The files are in the [http://www.geneontology.org/GO.format.shtml#oboflat OBO format] used by the [http://www.obofoundry.org/ Open Biomedical Ontology] group, and are designed to be used with the free [http://www.oboedit.org/ OBO-Edit] tool.<br />
<br />
Controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects. On the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page the frozen versions of the controlled vocabularies used for the current release of FlyBase are available, and there are also links to the current 'live' versions maintained by the [http://www.obofoundry.org/ Open Biomedical Ontology] group.<br />
<br />
Frozen versions of the controlled vocabularies used for previous releases of FlyBase are available on the "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" page, and in the following directories of the FTP repository:<br />
<br />
ftp://ftp.flybase.net/releases/<RELEASE_NUMBER>/precomputed_files/ontologies/<br />
<br />
For example see:<br />
<br />
ftp://ftp.flybase.net/releases/FB2008_03/precomputed_files/ontologies/<br />
<br />
===FASTA files===<br />
<br />
The FlyBase FASTA files generally follow the [http://en.wikipedia.org/wiki/Fasta_format FASTA format] guidelines with one exception being that our header lines sometime exceed the 80 character limit. The FASTA filenames follow these formats:<br />
<br />
'''dmel-all-<data type>-r<release-number>.fasta.gz'''<br />
<br />
or<br />
<br />
'''dmel-<chromosome_arm>-<data_type>-r<release-number>.fasta.gz'''<br />
<br />
Where '''data_type''' is one of the following entries in the table below. The '''all''' files contain sequences for those data types on all chromosome arms whereas the specific chromosome arm have only those features for that particular chromosome. <br />
<br />
{| class= "wikitable"<br />
!Data Type <br />
!Content Description<br />
|-<br />
|'''aligned ''' <br />
|The region of genomic sequence that analysis features align to.<br />
|-<br />
|'''CDS''' <br />
|The contiguous protein coding sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.<br />
|-<br />
|'''chromosome'''<br />
|The sequence of each chromosome arm.<br />
|-<br />
|'''clones''' <br />
|The sequence of full length cDNA, 3' and 5' ESTs, and partial length clones.<br />
|-<br />
|'''exon ''' <br />
|The sequence of each exon split up into individual FASTA records.<br />
|-<br />
|'''five_prime_UTR'''<br />
|The sequence of 5' untranslated regions.<br />
|-<br />
|'''gene''' <br />
|The sequence of the gene span.<br />
|-<br />
|'''gene_extended2000''' <br />
|The sequence of the gene span with 2000 base pairs added upstream and downstream.<br />
|-<br />
|'''intergenic'''<br />
|The sequence of chromosomal regions between genes that do not contain known gene models.<br />
|-<br />
|'''intron''' <br />
|The sequence of each intron split up into individual FASTA records.<br />
|-<br />
|'''miRNA''' <br />
|The sequence of transcripts that are typed as micro RNAs.<br />
|-<br />
|'''miscRNA''' <br />
|The sequence of transcripts that are typed as small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), or ribosomal RNA (rRNA). May also contain other transcript types that do not exist in their own individual files.<br />
|-<br />
|'''ncRNA''' <br />
|The sequence of transcripts that are typed as non coding RNAs (ncRNA).<br />
|-<br />
|'''predicted''' <br />
|The sequence of various features that are derived from a variety of prediction algorithms. These can encompass analyses conducted by FlyBase or by 3rd party groups.<br />
|-<br />
|'''pseudogene''' <br />
|The sequence of transcripts that are typed as pseudogenes.<br />
|-<br />
|'''sequence_features''' <br />
|The sequence of sequence features, which currently describe data about RNAi reagents. In the future, it will also contain natural genomic features (aside from transcribed regions), such as replication origins, transcription factor binding sites and boundary elements, and other experimental reagents that map to the genome, such as microarray oligonucleotides and rescue fragments.<br />
|-<br />
|'''synteny'''<br />
|The sequence of syntenic regions between two species.<br />
|-<br />
|'''three_prime_UTR'''<br />
|The sequence of 3' untranslated regions.<br />
|-<br />
|'''transcript'''<br />
|The sequence of transcripts that are typed as messenger RNAs (mRNA).<br />
|-<br />
|'''translation''' <br />
|The resulting protein sequence from protein coding transcripts.<br />
|-<br />
|'''transposon'''<br />
|The sequence of transposable elements.<br />
|-<br />
|'''tRNA''' <br />
|The sequence of transcripts that are typed as transfer RNAs (tRNA).<br />
|}<br />
<br />
<br />
====FASTA header format====<br />
<br />
The typical format of our FASTA header begins with an ID followed by any number of fields that follow this format<br />
<br />
'''field_name=value;'''<br />
<br />
Multiple field values are separated by commas<br />
<br />
'''field_name=value1,value2;'''<br />
<br />
This table describes some of the field names found in our FASTA headers <br />
<br />
{|class = "wikitable"<br />
<br />
!Field Name<br />
!Description<br />
|-<br />
|'''type''' <br />
|The feature type of the FASTA sequence record.<br />
|-<br />
|'''loc''' <br />
|The genomic location given in the NCBI's feature location format. Please see the [ftp://ftp.ncbi.nih.gov/genbank/docs/ NCBI's] site for more information.<br />
|-<br />
|'''ID''' <br />
|A unique ID. IDs in the form of FBxx[0-9]+ are a unique FlyBase object identifier.<br />
|-<br />
|'''name'''<br />
|The name or symbol of the feature.<br />
|-<br />
|'''dbxref'''<br />
|Database cross references relating to the FASTA record. The dbxref values use a 'dbname:dbid' format.<br />
|-<br />
|'''MD5'''<br />
|An [http://en.wikipedia.org/wiki/MD5 MD5] checksum calculated from the sequence that can be used to identify identical sequences.<br />
|-<br />
|'''length'''<br />
|The length of the sequence found in the FASTA record.<br />
|-<br />
|'''release'''<br />
|The release number denotes the annotation release which this FASTA record corresponds to.<br />
|-<br />
|'''species'''<br />
|The species abbreviation that this FASTA record corresponds to.<br />
|}<br />
<br />
<br />
===GFF files===<br />
<br />
The FlyBase GFF files follow the [http://www.sequenceontology.org/gff3.shtml GFF v3] specification. The GFF files contain feature line definitions for gene models, predicted features, alignments, and many other features. The GFF files are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gff/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gff/<br />
<br />
For melanogaster, there are 3 GFF files distributed, they include:<br />
<br />
:'''dmel-all-r<release-number>.gff.gz'''<br />
::Contains all chromosome arms<br />
:'''dmel-all-no-analysis-r<release-number>.gff.gz'''<br />
::Same as above except all match and match_part features have been removed<br />
:'''dmel-<chromosome_arm>-r<release-number>.gff.gz'''<br />
::Contains only a single chromosome arm as identifed by the filename<br />
<br />
The other species have the all chromosome arm file and also a tar and gzipped file containing the individual scaffolds. Please note that the tarball contains thousands of files in a single directory level so extracting them may result in filesystem performance issues. <br />
<br />
===GTF files===<br />
<br />
The FlyBase GTF files follow the [http://mblab.wustl.edu/GTF22.html GTF v2.2] specification. The GTF files contain feature line definitions for gene models. The GTF are produced for each species and can be downloaded from our FTP site using this URL form:<br />
<br />
ftp://ftp.flybase.org/genomes/<species abbreviation>/current/gtf/<br />
<br />
e.g. ftp://ftp.flybase.org/genomes/dmel/current/gtf/<br />
<br />
===Precomputed data text files===<br />
<br />
Precomputed data files that contain useful sets of data are generated for every release of FlyBase. For example, the file fbgn_NAseq_Uniprot_fb_2008_10.tsv.gz contains the mapping between valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] and the corresponding nucleic acid and protein accession numbers used by DDBJ/EMBL/GenBank and UniprotKB/Swiss-Prot/TrEMBL. These files can be found under the "Other" heading of each section of the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" and "[http://{{flybaseorg}}/static_pages/downloads/archivedata3.html Archived data]" pages, and are also available under the precomputed_files directory of each FlyBase release in the [ftp://ftp.flybase.net/releases/ FTP repository].<br />
<br />
Superscripts and subscripts are represented in the precomputed data files in the ASCII text format used by FlyBase, which is described in [[FlyBase:Nomenclature#10.3|section 10.3]] of the Nomenclature document.<br />
<br />
At the top and bottom of each tab separated text file there are a few lines that describe the file. These lines start with a '#' symbol. The line immediately before the start of the data contains headings for each of the tab separated columns in the file. The file can also include some blank lines to separate information about the version of the file from the description of data in the file.<br />
<br />
Each precomputed data file available for download on the "[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]" page contains the complete data set for the FlyBase release. Please note, if you are only looking for information on a defined subset of genes, or other FlyBase data type, you can query the current set of precomputed data files through the [http://{{flybaseorg}}/batchdownload Batch Download] tool to obtain the data you require. This approach is described in more detail in [https://wiki.flybase.org/wiki/FlyBase:Batch_Download this] help document.<br />
<br />
==Contents of the precomputed data text files listed by section==<br />
<br />
===Main data set===<br />
<br />
====Postgres Chado database dump====<br />
=====Chado database (ftp://ftp.flybase.net/releases/current/psql)=====<br />
The entire SQL Chado database is available for download. Follow the "README" directions herein.<br />
<br />
====Drosophila data====<br />
=====Current FTP repository (ftp://ftp.flybase.net/releases/current/)=====<br />
All files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Current Chado-XML repository (ftp://ftp.flybase.net/releases/current/chado-xml)=====<br />
All Chado XML files for this current FlyBase release are available on this FTP site.<br />
<br />
=====Genomes FTP archive (ftp://ftp.flybase.net/genomes/)=====<br />
All FlyBase genome and genome annotation files are available for various Drosophila species. Formats include Chado XML, DNA, FASTA, GFF and GTF. Files from both the current release and previous FlyBase releases are offered. For release FB2018_05 and earlier, data is available for each of the original 12 sequenced Drosophila species. From release FB2018_06 onward, data is available only for D. melanogaster, D. simulans, D. ananassae, D. pseudoobscura and D. virilis.<br />
<br />
===Synonyms===<br />
<br />
====FlyBase Synonyms (fb_synonym_*.tsv)====<br />
The file reports current symbols and synonyms for the following objects in FlyBase: genes (FBgn), alleles (FBal), balancers (FBba), aberrations (FBab), transgenic constructs (FBtp), insertions (FBti), transcripts (FBtr), and proteins (FBpp).<br />
<br />
The file includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
* genes from drosophilid species and genes from non-drosophilids that have been introduced into transgenic flies<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''primary_FBid''' <br />
|Primary FlyBase identifier for the object.<br />
|-<br />
|'''organism_abbreviation''' <br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin.<br />
|-<br />
|'''current_symbol'''<br />
|Current symbol used in FlyBase for the object.<br />
|-<br />
|'''current_fullname''' <br />
|Current full name used in FlyBase for the object.<br />
|-<br />
|'''fullname_synonym(s)''' <br />
|Non-current full name(s) associated with the object (comma separated values).<br />
|-<br />
|'''symbol_synonym(s)'''<br />
|Non-current symbol(s) associated with the object (comma separated values).<br />
|-<br />
|}<br />
<br />
===Genes===<br />
<br />
====Genes data (Chado XML)====<br />
<br />
====Genetic interaction table (gene_genetic_interactions_*.tsv)====<br />
The file reports the summary of gene-level genetic interactions in FlyBase. This data is computed from the allele-level genetic interaction data captured by FlyBase curators.<br />
<br />
The file includes information for Dmel genes only.<br />
<br />
Interactions involving any of the following kinds of allele are considered when the gene-level genetic interaction data is computed:<br />
<br />
* classical mutations<br />
* alleles carried on transgenic constructs<br />
* loss-of-function mutations<br />
* gain-of-function mutations<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Starting_gene(s)_symbol''' <br />
|Current FlyBase symbol of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Starting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the starting genotype.<br />
|-<br />
|'''Interacting_gene(s)_symbol'''<br />
|Current FlyBase symbol of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interacting_gene(s)_FBgn''' <br />
|Current FlyBase identifier (FBgn#) of gene(s) involved in the interacting genotype.<br />
|-<br />
|'''Interaction_type''' <br />
|Type of interaction observed, either 'suppressible' or 'enhanceable'.<br />
|-<br />
|'''Publication_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if the same genetic interaction has been reported in multiple references, multiple rows will exist for that genetic interaction in the file.<br />
<br />
* 'suppressible' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are suppressed by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
* 'enhanceable' in column 5 indicates that phenotypes caused by mutation of the gene(s) listed in the starting genotype (column 1) are enhanced by mutation of the gene(s) listed in the interacting genotype (column 3).<br />
<br />
''e.g.''<br />
<br />
Pten&emsp;FBgn0026379&emsp;Akt1&emsp;FBgn0010379&emsp;suppressible&emsp;FBrf0127089<br />
<br />
indicates that phenotype(s) caused by a mutation of Pten are suppressed by a mutation of Akt1.<br />
<br />
* For cases where multiple genes are simultaneously mutated in either (or both) the starting and interacting genotype, then the genes involved are separated by a '|' in the relevant columns. In this case, the order of the list of symbols and of the list of ids in columns 1 and 2, or in columns 3 and 4 respectively are the same, so that the FBgn corresponding to the symbol for each gene can easily be identified.<br />
<br />
''e.g.''<br />
<br />
robo1|sli&emsp;FBgn0005631|FBgn0264089&emsp;RhoGAP93B&emsp;FBgn0038853&emsp;enhanceable&emsp;FBrf0191476<br />
<br />
indicates that:<br />
* phenotype(s) caused by a robo1, sli double mutant combination are enhanced by a mutation of RhoGAP93B.<br />
* FBgn0005631 corresponds to robo1, FBgn0264089 corresponds to sli<br />
<br />
<br />
<br />
====RNA-Seq RPKM values (gene_rpkm_report_fb_*.tsv.gz)====<br />
This file reports gene expression values based on RNA-Seq experiments, calculated as reads per kilobase per million reads (RPKM). RPKM values are calculated only for the unique exonic regions of the gene (excluding segments that overlap other genes), except for genes derived from dicistronic/polycistronic transcripts, in which case all exon regions are used in the RPKM expression calculation.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Release_ID'''<br />
|The D. melanogaster annotation set version from which the gene model used in the analysis derives.<br />
|-<br />
|'''FBgn#'''<br />
|The unique FlyBase gene ID for this gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|The official FlyBase symbol for this gene.<br />
|-<br />
|'''Parent_library_FBlc#'''<br />
|The unique FlyBase ID for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''Parent_library_name'''<br />
|The official FlyBase symbol for the dataset project to which the RNA-Seq experiment belongs.<br />
|-<br />
|'''RNASource_FBlc#'''<br />
|The unique FlyBase ID for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RNASource_name'''<br />
|The official FlyBase symbol for the RNA-Seq experiment used for RPKM expression calculation.<br />
|-<br />
|'''RPKM_value'''<br />
|The RPKM expression value for the gene in the specified RNA-Seq experiment.<br />
|-<br />
|'''Bin_value'''<br />
|The expression bin classification of this gene in this RNA-Seq experiment, based on RPKM value. Bins range from 1 (no/extremely low expression) to 8 (extremely high expression).<br />
|-<br />
|'''Unique_exon_base_count'''<br />
|The number of exonic bases unique to the gene (not overlapping exons of other genes). Field will be blank for genes derived from dicistronic/polycistronic transcripts.<br />
|-<br />
|'''Total_exon_base_count'''<br />
|The number of bases in all exons of this gene.<br />
|-<br />
|'''Count_used'''<br />
|Indicates if the RPKM expression value was calculated using only the exonic regions unique to the gene and not overlapping exons of other genes (Unique), or, if the RPKM expression value was calculated based on all exons of the gene regardless of overlap with other genes (Total). RPKM expression values are typically reported for the "Unique" count, except for genes on dicistronic/polycistronic transcripts, in which case the "Total" count is reported.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Physical interaction table (physical_interactions_fb_*.tsv.gz)====<br />
This file reports unique gene pairs with curated support for some type of physical interaction. The file does not currently distinguish between genes that are involved in protein-protein or RNA-protein interactions (or both).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_FBgn1'''<br />
|The unique FlyBase gene ID for the first gene of the interacting pair.<br />
|-<br />
|'''gene_symbol1'''<br />
|The official FlyBase symbol for the first gene of the interacting pair.<br />
|-<br />
|'''gene_FBgn2'''<br />
|The unique FlyBase gene ID for the second gene of the interacting pair.<br />
|-<br />
|'''gene_symbol2'''<br />
|The official FlyBase symbol for the second gene of the interacting pair.<br />
|-<br />
|'''FBrf(s)'''<br />
|The unique FlyBase IDs for the publications supporting this interaction.<br />
|-<br />
|'''FBig_id'''<br />
|The unique FlyBase ID for this pairwise interaction.<br />
|-<br />
|'''#_reported_interactions'''<br />
|The number of distinct experiments in support of this interaction.<br />
|-<br />
|}<br />
<br />
<br />
====Physical interaction MITAB file (physical_interactions_mitab_fb_*.tsv.gz)====<br />
This file reports each individual experiment curated by FlyBase that supports a physical interaction between two gene products. There can be multiple experiments (multiple rows in the file) between products of the same gene pair. Interaction molecule types currently curated are protein-protein, protein-RNA or RNA-RNA. <br />
<br />
This file is in PSI-MI TAB format, a tab-delimited format developed by the HUPO Proteomics Standards Initiative (PSI) Molecular Interactions (MI) working group to facilitate interactomics data comparison and exchange. Details on the general MITAB format can be found [https://psicquic.github.io/MITAB27Format.html here]. The file makes use of the Molecular Interactions ontology which can be searched or browsed [https://www.ebi.ac.uk/ols/ontologies/mi here]. Fields are filled with “-” if values are missing or not relevant.<br />
<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading<br />
!General format <br />
!FlyBase example<br />
!Content description<br />
|-<br />
|'''1'''<br />
|'''ID(s) Interactor A'''<br />
|database:identifier<br />
|flybase:FBgn0002121<br />
|The unique Flybase identifier for the first gene of the interacting pair.<br />
|-<br />
|'''2'''<br />
|'''ID(s) Interactor B'''<br />
|”<br />
|”<br />
|The unique Flybase identifier for the second gene of the interacting pair.<br />
|-<br />
|'''3'''<br />
|'''Alt ID(s) Interactor A'''<br />
|database:identifier<br />
|<nowiki>flybase:CG2671|entrez gene/locuslink:33156</nowiki><br />
|<nowiki>The alternative gene identifiers currently provided are Flybase annotation IDs (CG#) and NCBI’s Entrez Gene ID separated by “|”.</nowiki><br />
|-<br />
|'''4'''<br />
|'''Alt ID(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''5'''<br />
|'''Alias(es) Interactor A'''<br />
|database:name(alias type)<br />
|flybase:l(2)gl(gene name)<br />
|The official Flybase gene symbol. It is referred to as “gene name” to adhere to the psi-mi ontology.<br />
|-<br />
|'''6'''<br />
|'''Alias(es) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''7'''<br />
|'''Interaction Detection Method(s)'''<br />
|ontology:identifier(method name)<br />
|psi-mi:"MI:0006"(anti bait coimmunoprecipitation)<br />
|The assay used to detect the interaction, taken from the psi-mi ontology.<br />
|-<br />
|'''8'''<br />
|'''Publication 1st Author(s)'''<br />
|surname initial(s) (publication year)<br />
|Betschinger K. (2003)<br />
|The first author and year of the publication where the interaction is described.<br />
|-<br />
|'''9'''<br />
|'''Publication ID(s)'''<br />
|database:identifier<br />
|<nowiki>flybase:FBrf0157155|pubmed:12629552</nowiki><br />
|<nowiki>The unique FlyBase identifier for the publication followed by the unique PubMed identifier (if there is one) separated by “|”.</nowiki><br />
|-<br />
|'''10'''<br />
|'''Taxid Interactor A'''<br />
|taxid:identifier<br />
|taxid:7227("Drosophila melanogaster")<br />
|The NCBI taxonomy identifier for the source organism of the interactor. The vast majority of interactors in FlyBase come from D. melanogaster. There are, however, a few interspecies interactions consisting of a D. melanogaster interactor and an interactor of a different species.<br />
|-<br />
|'''11'''<br />
|'''Taxid Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''12'''<br />
|'''Interaction Type(s)'''<br />
|ontology:identifier(interaction type)<br />
|psi-mi:"MI:0915"(physical association)<br />
|Taken from the psi-mi ontology. Most often “physical association” for FlyBase.<br />
|-<br />
|'''13'''<br />
|'''Source Database(s)'''<br />
|ontology:identifier(database name)<br />
|psi-mi:"MI:0478"(flybase)<br />
|All interactions are curated by FlyBase.<br />
|-<br />
|'''14'''<br />
|'''Interaction Identifier(s)'''<br />
|database:identifier<br />
|flybase:FBrf0157155-13.coIP.WB<br />
|The unique FlyBase identifier for this interaction.<br />
|-<br />
|'''15'''<br />
|'''Confidence Value(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''16'''<br />
|'''Expansion Method(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''17'''<br />
|'''Biological Role(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''18'''<br />
|'''Biological Role(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''19'''<br />
|'''Experimental Role(s) Interactor A'''<br />
|ontology:identifier(experimental role name)<br />
|psi-mi:"MI:0496"(bait)<br />
|The role played by the interactor in the experiment. Taken from the psi-mi ontology.<br />
|-<br />
|'''20'''<br />
|'''Experimental Role(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''21'''<br />
|'''Type(s) Interactor A'''<br />
|ontology:identifier(interactor type name)<br />
|psi-mi:"MI:0326"(protein)<br />
|The molecule type. For FlyBase, these are limited to protein or ribonucleic acid. Taken from the psi-mi ontology.<br />
|-<br />
|'''22'''<br />
|'''Type(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''23'''<br />
|'''Xref(s) Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''24'''<br />
|'''Xref(s) Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''25'''<br />
|'''Interaction Xref(s)'''<br />
|database:identifier<br />
|flybase:FBig0000000103<br />
|<nowiki>Cross references for the interactions. For Flybase, these include an interaction group identifier (FBig) and possibly a collection identifier (FBlc) separated by “|”. All experiments that show an interaction between the products of gene A and gene B are compiled into an A-B interaction group, such that all interactions are associated with an interaction group identified by an FBig number. Interactions identified as part of a large scale study are also associated with the collection identifier, or FBlc number.</nowiki><br />
|-<br />
|'''26'''<br />
|'''Annotation(s) Interactor A'''<br />
|topic:text<br />
|isoform-comment:a isoform<br />
|Information on whether the interaction is specific to a particular interactor isoform.<br />
|-<br />
|'''27'''<br />
|'''Annotation(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''28'''<br />
|'''Interaction Annotation(s)'''<br />
|topic:text<br />
|molecular source:Source was cell extract of S2 cell line; bait produced from endogenous gene; prey produced from endogenous gene.|comment:Phosphorylated isoforms of @l(2)gl@ are absent when @aPKC@ is knocked down by RNAi.<br />
|Describes the source(s) of the interaction participants and includes free text comments about the interaction.<br />
|-<br />
|'''29'''<br />
|'''Host Organism(s)'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''30'''<br />
|'''Interaction Parameters'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''31'''<br />
|'''Creation Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''32'''<br />
|'''Update Date'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''33'''<br />
|'''Checksum Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''34'''<br />
|'''Checksum Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''35'''<br />
|'''Interaction Checksum'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''36'''<br />
|'''Negative'''<br />
|<br />
|FALSE<br />
|All interactions in FlyBase are positive.<br />
|-<br />
|'''37'''<br />
|'''Feature(s) Interactor A'''<br />
|feature_type:range(text)<br />
|sufficient binding region:aa 1-58(N-terminal region)<br />
|Describes features of Interactor A such as binding sites, mutations that disrupt the interaction, epitope tags, etc.<br />
|-<br />
|'''38'''<br />
|'''Feature(s) Interactor B'''<br />
|”<br />
|”<br />
|”<br />
|-<br />
|'''39'''<br />
|'''Stoichiometry Interactor A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''40'''<br />
|'''Stoichiometry Interactor B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''41'''<br />
|'''Identification Method(s) Participant A'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|'''42'''<br />
|'''Identification Method(s) Participant B'''<br />
|<br />
|<br />
|Not applicable<br />
|-<br />
|}<br />
<br />
<br />
====Functional complementation table (gene_functional_complementation_*.tsv)====<br />
<br />
This file reports when functional complementation of Dmel genes by non-Dmel orthologs has been observed. This data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature. The file contains a list of gene Dmel - to - non-Dmel-ortholog gene pairs where a transgenic construct/mutant allele of the non-Dmel ortholog has been shown to at least partially suppress mutant phenotype(s) of an allele of the Dmel gene.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''Dmel gene (symbol)'''<br />
|Current FlyBase symbol of Dmel gene.<br />
|-<br />
|'''2'''<br />
|'''Dmel gene (FBgn)'''<br />
|Current FlyBase identifier (FBgn#) of Dmel gene in column 1.<br />
|-<br />
|'''3'''<br />
|'''Functionally complementing ortholog (symbol)'''<br />
|Current FlyBase symbol of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''4'''<br />
|'''Functionally complementing ortholog (FBgn#)'''<br />
|Current FlyBase identifier (FBgn#) of a non-Dmel ortholog of the Dmel gene in column 1 where this non-Dmel gene has been show to functionally complement the Dmel gene.<br />
|-<br />
|'''5'''<br />
|'''Supporting_FBrf'''<br />
|Current FlyBase identifier (FBrf#) of the publication that provides support for the functional complementation statement (the publication that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information from a single reference. Thus if multiple references support the same functional complementation statement, multiple rows will exist for that statement in the file.<br />
<br />
<br />
====FBgn <=> DB Accession IDs (fbgn_NAseq_Uniprot_*.tsv)====<br />
The file reports EMBL/GenBank/DDBJ nucleotide and protein accessions, UniProtKB/SwissProt/TrEMBL protein accessions, NCBI Entrez gene IDs and NCBI RefSeq transcript and protein accessions associated with FlyBase genes.<br />
<br />
The file includes:<br />
* nuclear genes with sequence accession numbers<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes without sequence accession numbers<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column number<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''1'''<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''2'''<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''3'''<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''4'''<br />
|'''nucleotide_accession'''<br />
|EMBL/GenBank/DDBJ nucleotide accession associated with the gene.<br />
|-<br />
|'''5'''<br />
|'''na_based_protein_accession'''<br />
|EMBL/GenBank/DDBJ protein accession associated with the gene and the nucleotide accession in the preceeding 'nucleotide_accession' column<br />
|-<br />
|'''6'''<br />
|'''UniprotKB/Swiss-Prot/TrEMBL_accession'''<br />
|UniProtKB/SwissProt/TrEMBL protein accession associated with the gene.<br />
|-<br />
|'''7'''<br />
|'''EntrezGene_ID'''<br />
|NCBI Entrez ID associated with the gene.<br />
|-<br />
|'''8'''<br />
|'''RefSeq_transcripts'''<br />
|NCBI RefSeq transcript accession associated with the gene.<br />
|-<br />
|'''9'''<br />
|'''RefSeq_proteins'''<br />
|NCBI RefSeq protein accession associated with the gene and the transcript accession in the preceeding 'RefSeq_transcripts' column.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single accession associated with a gene, thus if a gene has multiple accessions associated with it, multiple rows will exist for that gene in the file.<br />
<br />
* A single row contains '''only''' information about an EMBL/GenBank/DDBJ accession '''or''' information about a UniProtKB/SwissProt/TrEMBL accession '''or''' an NCBI Entrez gene ID '''or''' an NCBI RefSeq transcript accession.<br />
<br />
* For rows containing information about a EMBL/GenBank/DDBJ accession, a nucleotide accession associated with the gene is listed in column 4 ('nucleotide_accession'). If there is also a EMBL/GenBank/DDBJ protein accession associated with that gene '''and''' with the nucleotide accession in column 4, this protein accession is listed in column 5 ('na_based_protein_accession'). In this case, columns 6, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about a UniProtKB/SwissProt/TrEMBL protein accession, a protein accession associated with the gene is listed in column 6 ('UniprotKB/Swiss-Prot/TrEMBL_accession'). In this case, columns 4, 5, 7, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI Entrez gene, an ID associated with the gene is listed in column 7 ('EntrezGene_ID'). In this case, columns 4, 5, 6, 8 and 9 are always empty.<br />
<br />
* For rows containing information about an NCBI RefSeq accession, a transcript accession associated with the gene is listed in column 8 ('RefSeq_transcripts'). If there is also an NCBI RefSeq protein accession associated with that gene '''and''' with the transcript accession in column 8, this protein accession is listed in column 9 ('RefSeq_proteins'). In this case, columns 4, 5, 6 and 7 are always empty.<br />
<br />
<br />
<br />
====FBgn <=> Annotation ID (fbgn_annotation_ID_*.tsv)====<br />
The file reports current and secondary FlyBase identifiers associated with FlyBase genes, including current and secondary gene identifiers (FBgn#), and current and secondary annotation identifiers (CG#).<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''gene_symbol'''<br />
|Current symbol of gene.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''secondary_FBgn#(s)'''<br />
|Secondary FlyBase identifier(s) (FBgn#) associated with the gene (comma separated values).<br />
|-<br />
|'''annotation_ID'''<br />
|Current annotation identifier associated with the gene.<br />
|-<br />
|'''secondary_annotation_ID(s)'''<br />
|Secondary annotation identifier(s) associated with the gene (comma separated values).<br />
|-<br />
|}<br />
Notes:<br />
<br />
* If a gene has multiple secondary identifiers, all the values are stored within one tab separated column and are separated by commas (for example as: FBgn0034701,FBgn0034702). <br />
<br />
<br />
<br />
====FBgn <=> GLEANR IDs (fbgn_gleanr_*.tsv)====<br />
This file reports the relationship between the symbols and gene identifiers used by FlyBase for non-melanogaster genes identified by the AAA consortium, and the GLEANR identifier assigned to the gene during the initial annotation of the genome sequence.<br />
<br />
The file includes:<br />
* non-melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* ''D. melanogaster'' genes<br />
* non-melanogaster genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''gene_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBgn#'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GLEANR_ID'''<br />
|GLEANR identifier assigned by the AAA Consortium.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====FBgn <=> FBtr <=> FBpp IDs (fbgn_fbtr_fbpp_*.tsv)====<br />
This file reports the relationship of gene identifiers used by FlyBase for sequence localized genes, and the identifiers used for the transcript and polypeptide products of these genes.<br />
<br />
The file includes:<br />
* genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FlyBase_FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FlyBase_FBtr'''<br />
|Current FlyBase identifier (FBtr#) of a transcript encoded by the gene listed in the preceeding 'FlyBase_FBgn' column.<br />
|-<br />
|'''FlyBase_FBpp'''<br />
|Current FlyBase identifier (FBpp#) of a polypeptide encoded by the transcript listed in the preceeding 'FlyBase_FBtr' column, where this is relevant.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single transcript and the polypeptide it encodes (if relevant). Thus if a gene encodes multiple isoforms, multiple rows with exist for that gene in the file.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy1 (fbgn_exons2affy1_overlaps.tsv)====<br />
The file is generated by testing for overlaps, no matter how small, of the locations of Affy1 oligos in the genome with the locations of gene exons, as defined by the '''Dmel''' gene models for the current release of FlyBase. If the location of an Affy1 oligo shows any kind of overlap with an exon of a gene, a Gene=>Affy reference is recorded in this file.<br />
<br />
The extent of the overlap has no influence on the inclusion of a crossreference in this file. The overlap might be just one nucleotide, or it could be an exact match to the exon. For interpretation of the significance of a partial overlap please contact Affymetrix.<br />
<br />
The file includes the following '''Dmel''' genes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
Notes:<br />
<br />
* Each line of the file '''can contain many''' tab separated columns:<br />
<br />
* '''The first column of a line''' contains the valid [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifiers]] of a gene.<br />
* '''Subsequent columns:''' Each '''Affy1 ID''' that overlaps with an exon of the gene, as described above, is listed in an additional tab separated column. Thus, this file does not contain a predefined number of columns.<br />
<br />
<br />
<br />
====FBgn exons <=> Affy2 (fbgn_exons2affy2_overlaps.tsv)====<br />
The file is generated from the location of Affy2 oligos exactly as [[FlyBase:FilesOverview#5.2.6|described for Affy1 oligos]] above.<br />
<br />
<br />
<br />
====Genes GO data (gene_association.fb)====<br />
The file contains the [http://www.geneontology.org/ Gene Ontology] (GO) controlled vocabulary (CV) terms assigned to FlyBase genes.<br />
<br />
The file includes the following Dmel genes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
The columns of the file are described in [[FlyBase:Gene Ontology (GO) Annotation|section G.3.1.]] of the Reference manual.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_*.tsv)====<br />
The file reports available localization information for FlyBase genes.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the gene.<br />
|-<br />
|'''current_symbol'''<br />
|Current FlyBase gene symbol.<br />
|-<br />
|'''primary_FBid'''<br />
|Current FlyBase identifier (FBgn#) of gene.<br />
|-<br />
|'''recombination_loc'''<br />
|recombination map location.<br />
|-<br />
|'''cytogenetic_loc'''<br />
|cytogenetic location.<br />
|-<br />
|'''sequence_loc'''<br />
|genomic location.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Automated gene summaries (automated_gene_summaries.tsv)====<br />
The file contains the summaries found on gene report pages and the pop-ups in GBrowse and Interactions Browser in plain text.<br />
<br />
It includes:<br />
<br />
* nuclear genes located to the sequence<br />
* mitochondrial genes<br />
* genes not located to the sequence<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|FlyBase ID. The Valid FlyBase identifier number for the gene.<br />
|-<br />
|'''-'''<br />
|The gene summary as a string of plain text.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Gene Snapshots (gene_snapshots_*.tsv)====<br />
The file contains in plain text the gene snapshot information visible on gene report pages.<br />
<br />
It includes only Dmel protein coding genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier number for the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase symbol of the gene.<br />
|-<br />
|'''GeneName'''<br />
|Current FlyBase name of the gene.<br />
|-<br />
|'''datestamp'''<br />
|Date on which the information was last reviewed.<br />
|-<br />
|'''gene_snapshot_text'''<br />
|Gene snapshot information for the gene. Cases that are in progress or are deemed to have insufficient data to summarize are stated as such.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Unique protein isoforms (dmel_unique_protein_isoforms_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their unique protein isoforms.<br />
<br />
The file includes:<br />
* melanogaster genes located to the sequence<br />
<br />
it excludes:<br />
* melanogaster genes not located to the sequence<br />
* non-melanogaster genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''FB_gene_symbol'''<br />
|Current FlyBase gene symbol of the gene.<br />
|-<br />
|'''representative_protein'''<br />
|Current FlyBase protein symbol of the representative protein isoform.<br />
|-<br />
|'''identical_protein(s)'''<br />
|Current FlyBase protein symbol(s) of identical protein isoforms.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNA genes (TSV) (ncRNA_genes_fb_*.tsv.gz)====<br />
This file reports all genes encoding ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in TSV format. Pseudogenes are excluded.<br />
<br />
Columns are:<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''accession_id'''<br />
|INSDC accession ID.<br />
|-<br />
|'''FB_gene_ID'''<br />
|Current FlyBase gene identifier (FBgn#).<br />
|-<br />
|'''species_FB_annotation_ID(locus_tag)'''<br />
|Current FlyBase annotation ID, in the form "<species abbreviation>_<annotation_ID>", which equates to the 'locus tag' field in INSDC records.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Gene groups===<br />
====Gene group data (gene_group_data_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with their hierarchical relationships (where relevant) and member genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''Parent_FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Parent_FB_group_symbol'''<br />
|Current FlyBase symbol of parent of given Gene Group (if relevant).<br />
|-<br />
|'''Group_member_FB_gene_id'''<br />
|Current FlyBase identifier (FBgn##) of member gene (if terminal group).<br />
|-<br />
|'''Group_member_FB_gene_symbol'''<br />
|Current FlyBase symbol of member gene (if terminal group).<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Where groups are arranged into hierarchies:<br />
** the member genes are only associated with the terminal subgroups,<br />
** the immediate parent of any subgroup is identified in the ‘Parent_FB_group_id' and 'Parent_FB_group_symbol' columns.<br />
<br />
* Separate lines are used for each member gene, meaning that each terminal group is listed multiple times (equal to the number of member genes).<br />
<br />
<br />
<br />
====Gene groups with HGNC IDs (gene_groups_HGNC_*.tsv)====<br />
This file reports all Gene Groups in FlyBase, together with the corresponding HGNC 'gene family' ID (where relevant).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FB_group_id'''<br />
|Current FlyBase identifier (FBgg##) of Gene Group.<br />
|-<br />
|'''FB_group_symbol'''<br />
|Current FlyBase symbol of Gene Group.<br />
|-<br />
|'''FB_group_name'''<br />
|Current FlyBase full name of Gene Group.<br />
|-<br />
|'''HGNC_family_ID'''<br />
|HGNC ID of equivalent human 'gene family'.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* The absence of an HGNC_family_ID entry indicates there is no equivalent HGNC gene family for that FlyBase gene group.<br />
<br />
* Because of different sub-group structures (etc), a single HGNC family may be associated with multiple FlyBase gene groups.<br />
<br />
* Similarly, a single FlyBase gene group may be associated with multiple HGNC gene families - these are shown on separate lines.<br />
<br />
<br />
<br />
===Alleles and Stocks===<br />
====Allele data (Chado XML)====<br />
<br />
====Stock data (Chado XML)====<br />
<br />
====Stock data (stocks_*.tsv.gz)====<br />
This file reports genetic components and related information about Stocks in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
!Example<br />
|-<br />
|'''FBst'''<br />
|The unique identifier assigned to this stock by FlyBase.<br />
|FBst0000002<br />
|-<br />
|'''collection_short_name'''<br />
|A short name for the stock collection that holds the stock.<br />
|Bloomington<br />
|-<br />
|'''stock_type_cv'''<br />
|The controlled vocabulary term and unique identifier that describe the state of the stock.<br />
|living stock ; FBsv:0000002<br />
|-<br />
|'''species'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of the stock.<br />
|Dmel<br />
|-<br />
|'''FB_genotype'''<br />
|Genetic components of the stock corresponding to alleles, aberrations, balancers, or insertions in FlyBase. May be empty.<br />
|w[*]; betaTub60D[2] Kr[If-1]/CyO<br />
|-<br />
|'''description'''<br />
|Genetic components of the stock as provided to FlyBase by the collection that holds the stock.<br />
|FlyTrap: ZCL1796 III<br />
|-<br />
|'''stock_number'''<br />
|The stock identifier provided to FlyBase by the collection that holds the stock. May be empty.<br />
|110818<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genetic interactions (allele_genetic_interactions_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) genetic interaction data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Interactions" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''interaction'''<br />
|Interaction information associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row contains information about a single interaction from a single reference. Thus if multiple genetic interactions have been reported for a given allele, or if multiple references report the same interaction for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Phenotypic data (allele_phenotypic_data_*.tsv)====<br />
The file reports controlled vocabulary (i.e. not free text) phenotypic data associated with alleles. This is the data reported in the "Phenotypic Class" and "Phenotype Manifest in" subsections of the "Phenotypic Data" section of each Allele Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''allele_symbol'''<br />
|Current FlyBase allele symbol.<br />
|-<br />
|'''allele_FBal#'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''phenotype'''<br />
|Phenotypic data associated with allele.<br />
|-<br />
|'''FBrf#'''<br />
|Current FlyBase identifer (FBrf#) of publication from which data came.<br />
|-<br />
|}<br />
<br />
Notes: <br />
<br />
* Each row contains information about a single phenotype from a single reference. Thus if multiple phenotypes have been reported for a given allele, or if multiple references report the same phenotype for a given allele, multiple rows will exist for that allele in the file.<br />
<br />
<br />
<br />
====Alleles <=> Genes (fbal_to_fbgn_fb_*.tsv)====<br />
This file reports the relationship between gene identifiers and the identifiers used for alleles of these genes.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''AlleleID'''<br />
|Current FlyBase identifier (FBal#) of the allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current symbol of the allele.<br />
|-<br />
|'''GeneID'''<br />
|Current FlyBase identifier (FBgn#) of the gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current symbol of the gene.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Orthologs===<br />
<br />
====Drosophila Orthologs (dmel_orthologs_in_drosophila_species_fb_*.tsv.gz)====<br />
The file reports ''D. melanogaster'' genes and their orthologs in other sequenced Drosophila genomes, as determined by OrthoDB. (The version of OrthoDB currently being used is shown in the 'Orthologs' -> 'Orthologs (via OrthoDB)' section of a Gene Report.)<br />
<br />
The file includes:<br />
* nuclear genes located to the sequence<br />
<br />
it excludes:<br />
* genes not located to the sequence<br />
* mitochondrial genes<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''GeneSymbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Arm/Scaffold'''<br />
|Arm upon which the ''D. melanogaster'' gene is localized.<br />
|-<br />
|'''Location'''<br />
|Location of ''D. melanogaster'' gene on the arm.<br />
|-<br />
|'''Strand'''<br />
|Strand of ''D. melanogaster'' gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''Ortholog_FBgn_ID'''<br />
|Current FlyBase identifier (FBgn#) of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_GeneSymbol'''<br />
|Current FlyBase gene symbol of the non-melanogaster orthologous gene.<br />
|-<br />
|'''Ortholog_Arm/Scaffold'''<br />
|Arm upon which the non-melanogaster orthologous gene is localized.<br />
|-<br />
|'''Ortholog_Location'''<br />
|Location of non-melanogaster orthologous gene on the arm.<br />
|-<br />
|'''Ortholog_Strand'''<br />
|Strand of non-melanogaster orthologous gene ('1' indicates the positive strand, '-1' indicates the negative strand).<br />
|-<br />
|'''OrthoDB_Group_ID'''<br />
|OrthoDB orthology group ID to which the pair-wise association belongs.<br />
|-<br />
|}<br />
<br />
Notes:<br />
<br />
* Each row is a pair-wise association beween a ''D. melanogaster'' gene and a non-melanogaster ortholog. Thus, multiple rows exist for each ''D. melanogaster'' gene in the file.<br />
<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dmel_gene_ID'''<br />
|Current FlyBase identifier (FBgn#) of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Dmel_gene_symbol'''<br />
|Current FlyBase gene symbol of the ''D. melanogaster'' gene.<br />
|-<br />
|'''Human_gene_HGNC_ID'''<br />
|HGNC ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_OMIM_ID'''<br />
|OMIM ID of orthologous human gene.<br />
|-<br />
|'''Human_gene_symbol'''<br />
|HGNC gene symbol of orthologous human gene.<br />
|-<br />
|'''DIOPT_score'''<br />
|DIOPT 'score' for orthology call (i.e. the number of individual algorithms that support the call).<br />
|-<br />
|'''OMIM_Phenotype_IDs'''<br />
|OMIM Phenotype ID of orthologous human gene (comma separated values).<br />
|-<br />
|'''OMIM_Phenotype_IDs[name]'''<br />
|OMIM Phenotype ID of orthologous human gene (with the corresponding OMIM name in square brackets). Multiple phenotype[name] entries are separated by a comma.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Human disease===<br />
<br />
====Human disease model data (allele_human_disease_model_data_fb_*.tsv.gz)====<br />
This file reports all experimental-based disease model annotations, associated with alleles, that have been curated for ''D. melanogaster''. 'Alleles' encompasses both classical alleles and transgenic alleles; the latter may relate to transgenic constructs of ''D. melanogaster'' genes or non-''D. melanogaster'' genes, often human genes. These are the data reported in the "Human Disease Model Data" -> "Disease Ontology" section of the Allele Report, which are repeated in the "Human Disease Model Data" -> "Alleles Reported to Model Human Disease (Disease Ontology)" section of the Gene Report.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBal_ID'''<br />
|Current FlyBase identifier (FBal#) of allele.<br />
|-<br />
|'''AlleleSymbol'''<br />
|Current FlyBase symbol of allele.<br />
|-<br />
|'''DOID_qualifier'''<br />
|Annotation qualifier - one of 'model of', 'ameliorates', 'exacerbates', 'DOES NOT model', 'DOES NOT ameliorate' or 'DOES NOT exacerbate'.<br />
|-<br />
|'''DOID_term'''<br />
|Disease Ontology term.<br />
|-<br />
|'''DOID_ID'''<br />
|Disease Ontology ID.<br />
|-<br />
|'''Evidence/interacting_alleles'''<br />
|Evidence code, with interacting allele(s) where appropriate. Evidence code is one of: 'inferred from mutant phenotype', 'in combination with', 'modeled by', 'is ameliorated by', 'is exacerbated by', 'is NOT ameliorated by' or 'is NOT exacerbated by'. Interacting alleles are give as 'FLYBASE:<allele_symbol>; FB:<FBal_ID>', with multiple alleles separated by a comma.<br />
|-<br />
|'''Reference_FBid'''<br />
|Current FlyBase identifier (FBrf#) of the publication from which the data came.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Human Orthologs (dmel_human_orthologs_disease_fb_*.tsv.gz)====<br />
<br />
This file reports the human orthologs of ''D. melanogaster'' genes using the DIOPT dataset. Each line reports a single orthologous pair, which means that each human and D. melanogaster gene can appear in multiple lines. Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score <3) have been removed. Human genes are also associated with diseases (OMIM phenotypes) using the OMIM dataset.<br />
<br />
This is identical to the file of the same name listed under the 'Orthologs' section above. <br />
<br />
<br />
<br />
===Nomenclature===<br />
<br />
====Species abbreviation list (species-ab.gz)====<br />
<br />
The species-abbreviations.txt file lists all the species for which FlyBase has some information. FlyBase includes gene reports for genes derived from species within the family Drosophilidae, as well as gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two ''D.melanogaster'' genes. In addition, information about non-Drosophilid species is also displayed in GBrowse, for example in the "Similarity: Proteins" evidence tier. Thus, the file contains information for both Drosophilid and non-Drosophilid species.<br />
<br />
There are 8 columns of data in the file, each separated by " | ".<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Internal_id'''<br />
|The Primary [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the organism.<br />
|-<br />
|'''Taxgroup'''<br />
|A grouping term, currently one of "drosophilid", "non-drosophilid eukaryote", "prokaryote", "transposable element" or "virus".<br />
|-<br />
|'''Abbreviation'''<br />
|The standard FlyBase prefix for the species. This abbreviation is used in FlyBase as the first part of the symbol (before the '\') of any object, e.g. a gene or allele, that originates from this species. This column may be blank, if data from a species is displayed in an evidence tier on [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] but no individual report page exists for that species in FlyBase.<br />
|-<br />
|'''Genus'''<br />
|The genus name of the organism.<br />
|-<br />
|'''Species name'''<br />
|The species name of the organism.<br />
|-<br />
|'''Common name'''<br />
|The common name of the organism. This column may be blank.<br />
|-<br />
|'''Comment'''<br />
|A free text field for additional comments. This column may be blank.<br />
|-<br />
|'''Ncbi-taxon-id'''<br />
|The [http://www.ncbi.nlm.nih.gov/taxonomy NCBI Taxonomy Database] Taxon ID for the organism. This column may be blank.<br />
|-<br />
|}<br />
<br />
An html version of this file is also available - see the [[FlyBase:Abbreviations|Species Abbreviations]] page.<br />
<br />
<br />
<br />
===Ontology Terms===<br />
====Frozen files used for this release of FlyBase====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
* FBdv: fly_development<br />
* FBcv: flybase controlled vocabulary<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
====Current 'Live' Files====<br />
<br />
List of ontologies available for download:<br />
<br />
* FBbt: fly_anatomy<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_anatomy.obo' version''<br />
* FBdv: fly_development<br />
''Note: link points to the ontology version fbbt-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'fly_development.obo' version''<br />
* FBcv: flybase controlled vocabulary<br />
''Note: link points to the ontology version fbcv-simple.obo, which lacks a few minor FlyBase specific changes that are present in the 'flybase_controlled_vocabulary.obo' version''<br />
* FBsv: stock ontology<br />
* GO: gene ontology<br />
* FBbi: image ontology<br />
* SO: sequence ontology<br />
* DO: human disease ontology<br />
<br />
<br />
===Genomes: Annotation and Sequence===<br />
====All Sequenced Drosophila Species====<br />
<br />
Links are available to the following FTP repositories:<br />
<br />
* Current FTP repository<br />
* Current FastA repository<br />
* Current GFF repository<br />
<br />
* FTP archive (previous releases)<br />
<br />
* Current list of individual FASTA files<br />
* Current list of individual GFF files<br />
<br />
For release FB2018_06 onward, the above links are available for the following sequenced Drosophila species:<br />
<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila melanogaster<br />
|Dmel<br />
|-<br />
|Drosophila ananassae<br />
|Dana<br />
|-<br />
|Drosophila pseudoobscura pseudoobscura<br />
|Dpse<br />
|-<br />
|Drosophila simulans<br />
|Dsim<br />
|-<br />
|Drosophila virilis<br />
|Dvir<br />
|-<br />
|}<br />
<br />
<br />
For earlier archived releases, the above links are also available for these additional species (other members of the original 12 sequenced Drosophila species):<br />
<br />
{| class= "wikitable"<br />
!Species name <br />
!Abbreviation<br />
|-<br />
|Drosophila erecta<br />
|Dere<br />
|-<br />
|Drosophila grimshawi<br />
|Dgri<br />
|-<br />
|Drosophila mojavensis<br />
|Dmoj<br />
|-<br />
|Drosophila persimilis<br />
|Dper<br />
|-<br />
|Drosophila sechellia<br />
|Dsec<br />
|-<br />
|Drosophila willistoni<br />
|Dwil<br />
|-<br />
|Drosophila yakuba<br />
|Dyak<br />
|-<br />
|}<br />
<br />
===Transcripts and Polypeptides===<br />
<br />
====Transcript data (Chado XML)====<br />
<br />
====Polypeptide data (Chado XML)====<br />
<br />
====Non-coding RNAs (JSON) (ncRNA_genes_fb_*.json.gz)====<br />
This file reports all ncRNAs for D. melanogaster and 11 other sequenced Drosophila species in JSON format, as submitted to [http://rnacentral.org/ RNAcentral]. Pseudogenes are excluded. In addition to the symbols and IDs for ncRNAs, this file also includes their associated gene, genomic location, sequence, Sequence Ontology classification, etc. The full schema for this file is available [https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json here].<br />
<br />
===Transposons, Transgenic Constructs, and Insertions===<br />
<br />
====Insertions (Chado XML)====<br />
====Transgenic Constructs (Chado XML)====<br />
<br />
<br />
====Transgenic construct maps (construct_maps.zip)====<br />
The construct_maps.zip file unpacks as a directory containing maps of recombinant constructs and transgenic transposons generated by FlyBase, that are based on the compiled sequence data curated by FlyBase. The name of each PNG image in the directory corresponds to the [[FlyBase:RefMan_F.#FlyBase_Identifier_Numbers|FlyBase identifier]] of the respective recombinant construct or transgenic transposon.<br />
<br />
'''Please note:''' For transgenic transposons, the image may be a map of the corresponding plasmid form.<br />
<br />
====Map data for insertions (insertion_mapping_*.tsv)====<br />
The insertion mapping table reports available localization information for '''Dmel''' insertions.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''insertion_symbol'''<br />
|Current symbol of insertion.<br />
|-<br />
|'''FBti#'''<br />
|Current FlyBase identifier (FBti#) of insertion<br />
.<br />
|-<br />
|'''genomic_location'''<br />
|Genomic location of insertion.<br />
|-<br />
|'''range'''<br />
|Range (t/f) indicates whether genomic location is range or single base.<br />
|-<br />
|'''orientation'''<br />
|Orientation (1/0) indicates orientation of insertion on chromosome.<br />
|-<br />
|'''estimated_cytogenetic_location'''<br />
|Estimated cytogenetic location based on correlation of genomic location and estimated genomic location of cytological bands.<br />
|-<br />
|'''observed_cytogenetic_location'''<br />
|Observed cytogenetic location reported in the literature.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Transposable elements (canonical set) (transposon_sequence_set.embl.txt)====<br />
This is a file of 'canonical' sequences of the transposable elements from Drosophila maintained by M. Ashburner.<br />
<br />
The first section of the file outlines the history and revisions to the file and also lists the current set of elements, their size and whether the subsequent sequence data is complete.<br />
<br />
The second section of the file, which is separated from the first by a line of "_" characters contains the sequence data of all the elements in [ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html EMBL format]. The record for each element starts with a line prefixed by "ID" and ends with a line containing "//".<br />
<br />
====Frequently-used GAL4 drivers table (JSON) (fu_gal4_table_fb_2018_06.json)====<br />
This file reports a list of all GAL4 drivers that have been curated to at least 21 references and/or are among 150 most frequently requested GAL4 stocks from the Bloomington Drosophila Stock Center, in JSON format. In addition to the symbols and IDs for Scer\GAL4 alleles, this file also includes their associated transposon or insertion, associated gene, expression pattern in controlled vocabulary stage and anatomy terms, stocks, and publications, all with IDs, as well as free text expression pattern descriptions. This file, except for publications and stocks, is also available in TSV format [[http://flybase.org/GAL4/freq_used_drivers.tsv|here]].<br />
<br />
===Aberrations===<br />
====Aberration data (Chado XML)====<br />
====Balancer data (Chado XML)====<br />
<br />
===Large dataset metadata===<br />
====Dataset metadata members (dataset_metadata_fb_*.tsv.gz)====<br />
This file lists all features that are associated with a dataset/collection (e.g., genes, cDNA clones, TF_binding_sites, Affymetrix probes).<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Dataset_Metadata_ID'''<br />
|The unique FlyBase ID for the dataset.<br />
|-<br />
|'''Dataset_Metadata_Name'''<br />
|The official FlyBase symbol for the dataset.<br />
|-<br />
|'''Item_ID'''<br />
|The unique FlyBase ID for the feature associated with this dataset.<br />
|-<br />
|'''Item_Name'''<br />
|The official FlyBase symbol for the feature associated with this dataset.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Clones===<br />
<br />
====Clone data (Chado XML)====<br />
<br />
====cDNAs: FBcl <=> acc. ID (cDNA_clone_data_*.tsv)====<br />
The file reports basic cDNA clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of cDNA clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''dataset_metadata_name'''<br />
|Name of dataset associated with clone.<br />
|-<br />
|'''cDNA_accession(s)'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|'''EST_accession(s)'''<br />
|EMBL/GenBank/DDBJ EST accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Genomic: FBcl <=> acc. ID (genomic_clone_data_*.tsv)====<br />
<br />
The file reports basic genomic clone data in FlyBase.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBcl#'''<br />
|Current FlyBase identifier (FBcl#) of genomic clone.<br />
|-<br />
|'''organism_abbreviation'''<br />
|Abbreviation (from the [[FlyBase:Abbreviations|Species Abbreviations]] list) indicating the species of origin of the clone.<br />
|-<br />
|'''clone_name'''<br />
|Clone name.<br />
|-<br />
|'''accession'''<br />
|EMBL/GenBank/DDBJ cDNA accession number.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===References===<br />
====Combined reference data (Chado XML)====<br />
====FlyBase FBrf <=> PubMed ID <=> PMCID <=> DOI (fbrf_pmid_pmcid_doi_fb_*.tsv.gz)====<br />
<br />
This file lists all publications in the FlyBase bibliography that have a PubMed ID. Additional identifiers are listed as applicable.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''FBrf'''<br />
|The unique FlyBase ID for this publication.<br />
|-<br />
|'''PMID'''<br />
|The unique PubMed ID for this publication.<br />
|-<br />
|'''PMCID'''<br />
|The unique PubMed Central ID for this publication, if applicable.<br />
|-<br />
|'''DOI'''<br />
|The digital object identifier assigned to the publication.<br />
|-<br />
|'''pub_type'''<br />
|The publication type (for example, paper, review, erratum, abstract, book, etc.)<br />
|-<br />
|'''miniref'''<br />
|A short citation listing the first author, year of publication, journal, volume, issue and page numbers.<br />
|-<br />
|'''pmid_added'''<br />
|The FlyBase release in which the publication was first incorporated into the FlyBase bibliography. Note: as this report first generated for fb_2012_01 release, all publications associated with a Pub Med ID prior to this release have pmid_added = fb_2011_10.<br />
|-<br />
|}<br />
<br />
<br />
<br />
===Drosophila researchers===<br />
Addresses of Drosophila researchers are copyrighted (GSA) material and only provided for official business of the Fly Board.<br />
<br />
===Map conversion tables===<br />
====Cytological <=> Sequence (genome-cyto-seq.txt)====<br />
This is a tab delimited file that FlyBase uses to relate sequence coordinates from release 5 of the ''Drosophila melanogaster'' sequence assembly to published cytogenetic map positions. A description of how this is calculated is provided in [[FlyBase:Computed_cytological_data|section G.5.1.]] of the Reference manual.<br />
<br />
The data for each chromosome arm is separated by a line starting with a '#' that lists the name of the chromosome arm and corresponding sequence scaffold.<br />
<br />
The columns in the file are:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''-'''<br />
|Cytogenetic map position as described by Bridges.<br />
|-<br />
|'''-'''<br />
|First sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|'''-'''<br />
|Last sequence coordinate for this map position in the sequence scaffold corresponding this chromosome arm.<br />
|-<br />
|}<br />
<br />
<br />
<br />
====Cytological <=> Genetic (cytotable.txt)====<br />
This is the table that FlyBase uses to infer a genetic map position from a published cytogenetic map position for Drosophila melanogaster.<br />
<br />
The first six lines of the file describe the contents of the file or are blank. The data in the file is organized with the cytological position in first four characters of a line followed by a run of spaces and then the genetic map position.<br />
<br />
<br />
====Cyto <=> Genetic <=> Seq (cyto-genetic-seq.tsv)====<br />
This is a tab separated file generated from the cytotable.txt and genome-cyto-seq.txt files that infers the relationship between published cytogenetic map positions, genetic map positions and release 6 sequence assembly coordinates for ''Drosophila melanogaster''. Please note that band numbers are not given in this file because they are absent in cytotable.txt.<br />
<br />
File format:<br />
<br />
{| class= "wikitable"<br />
!Column heading <br />
!Content Description<br />
|-<br />
|'''Cytogenetic map position'''<br />
|Cytogenetic map position.<br />
|-<br />
|'''Genetic map position'''<br />
|Genetic map position.<br />
|-<br />
|'''Sequence coordinates (release 6)'''<br />
|Sequence coordinates (release 6) for the interval.<br />
|-<br />
|'''R6 conversion notes'''<br />
|<br />
|-<br />
|}<br />
<br />
<br />
An html version of this file is also available - see the [http://{{flybaseorg}}/static_pages/docs/cytotable3.html Map Conversion Table] page.<br />
<br />
<br />
<br />
====Genes map table (gene_map_table_fb_*.tsv)====<br />
This is identical to the file listed under the genes section above.<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=169945FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2018-04-18T16:37:31Z<p>Sian: /* Posters */</p>
<hr />
<div>== Pamphlets and Handouts ==<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
----<br />
<br />
== Presentations (Talks from Meetings or Courses) ==<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=169944FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2018-04-18T16:35:50Z<p>Sian: /* Posters */</p>
<hr />
<div>== Pamphlets and Handouts ==<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
----<br />
<br />
== Presentations (Talks from Meetings or Courses) ==<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
[[Category:DONE]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:Gramates_Disease_ADRC2018.pdf&diff=169943File:Gramates Disease ADRC2018.pdf2018-04-18T16:32:17Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=File:Gramates_GAL4_ADRC2018.pdf&diff=169942File:Gramates GAL4 ADRC2018.pdf2018-04-18T16:31:39Z<p>Sian: </p>
<hr />
<div></div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169604FlyBase:Human Disease Model Report2018-01-02T20:48:09Z<p>Sian: /* Sources of Stocks */</p>
<hr />
<div>Last Updated: 15 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of multiple ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [https://bdsc.indiana.edu/stocks/hd/index.html BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
For human or mammalian transgene(s) used to model this disease, transgenic constructs presented as a table that consists of three columns (below). If there are ten or fewer constructs, all are listed. For larger numbers, a selected sample weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
For Drosophila gene(s) used to model this disease, transgenic constructs and associated alleles presented as a table that consists of three columns (below). All alleles of transgenic constructs associated with a disease ontology term are listed. Additional listings weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
For Drosophila gene(s) used to model this disease, all RNAi constructs; presented as a table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
For Drosophila gene(s) used to model this disease, alleles presented as a table that consists of four columns (below). All classical alleles associated with a disease ontology term and/or described as amorphic are listed; if no amorphic alleles have been reported, loss-of-function alleles are listed. <br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169602FlyBase:Human Disease Model Report2018-01-02T19:42:44Z<p>Sian: /* Specific Disease Summary */</p>
<hr />
<div>Last Updated: 15 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of multiple ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
For human or mammalian transgene(s) used to model this disease, transgenic constructs presented as a table that consists of three columns (below). If there are ten or fewer constructs, all are listed. For larger numbers, a selected sample weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
For Drosophila gene(s) used to model this disease, transgenic constructs and associated alleles presented as a table that consists of three columns (below). All alleles of transgenic constructs associated with a disease ontology term are listed. Additional listings weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
For Drosophila gene(s) used to model this disease, all RNAi constructs; presented as a table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
For Drosophila gene(s) used to model this disease, alleles presented as a table that consists of four columns (below). All classical alleles associated with a disease ontology term and/or described as amorphic are listed; if no amorphic alleles have been reported, loss-of-function alleles are listed. <br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169601FlyBase:Human Disease Model Report2018-01-02T19:40:46Z<p>Sian: /* Specific Disease Summary */</p>
<hr />
<div>Last Updated: 15 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606 Gene2Function (human gene)]<br />
<br />
[http://marrvel.org MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of multiple ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
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<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
For human or mammalian transgene(s) used to model this disease, transgenic constructs presented as a table that consists of three columns (below). If there are ten or fewer constructs, all are listed. For larger numbers, a selected sample weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
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'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
For Drosophila gene(s) used to model this disease, transgenic constructs and associated alleles presented as a table that consists of three columns (below). All alleles of transgenic constructs associated with a disease ontology term are listed. Additional listings weighted for availability of stocks, frequency of citations, and more recent citations.<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
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'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
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'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
For Drosophila gene(s) used to model this disease, all RNAi constructs; presented as a table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
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'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
For Drosophila gene(s) used to model this disease, alleles presented as a table that consists of four columns (below). All classical alleles associated with a disease ontology term and/or described as amorphic are listed; if no amorphic alleles have been reported, loss-of-function alleles are listed. <br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169585FlyBase:QuickSearch2017-12-21T16:47:45Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
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In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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===Controlled Vocabularies===<br />
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Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
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===Auto-completion===<br />
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The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
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The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
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The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [http://{{flybaseorg}}/rnaseq/rnaseq RNA-Seq overview page]. There are '''video tutorials''' available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Note, as the GO is an ontology, all child terms will possess the property of the parent, therefore consider using '''Records annotated with this term OR any of its CHILDREN TERMS''' to get a complete gene list.<br />
<br />
Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
'''You can search by disease using:'''<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
'''You can search by human disease-associated gene using:'''<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
'''You can search ''Drosophila melanogaster'' genes using:'''<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
'''The QuickSearch auto-completion feature is active in this tab; auto-completion works for''' <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa. A related '''video tutorial''' can be found at *[https://www.youtube.com/watch?v=JsNyrNG28M0 Using the Orthology search tool].<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169446FlyBase:QuickSearch2017-12-19T17:24:51Z<p>Sian: /* Expression tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [http://{{flybaseorg}}/rnaseq/rnaseq RNA-Seq overview page]. There are video tutorials available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=Ho_PZ4XB8y8&t=2s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169445FlyBase:QuickSearch2017-12-19T17:21:54Z<p>Sian: /* Expression tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
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In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
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Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile Search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [http://{{flybaseorg}}/rnaseq/rnaseq RNA-Seq overview page]. There are video tutorials available for [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq in GBrowse], [https://www.youtube.com/watch?v=KpJVkopUBDM&t=107s RNA-Seq Profile Search], and [https://www.youtube.com/watch?v=mcMpRxeX-KY RNA-Seq Similarity Search].<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
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The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Orthologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
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This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
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The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
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The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
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A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
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Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
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===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169444FlyBase:QuickSearch2017-12-19T16:54:46Z<p>Sian: /* Expression tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. You can find a more detailed description of these RNA-Seq search options on the [http://{{flybaseorg}}/rnaseq/rnaseq RNA-Seq overview page].<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169443FlyBase:QuickSearch2017-12-19T16:31:07Z<p>Sian: /* Expression tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169442FlyBase:QuickSearch2017-12-19T16:17:32Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
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The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Orthologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
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This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
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The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
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The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
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A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
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Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
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===Protein Domains tab===<br />
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Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
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To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
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===References tab===<br />
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This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169441FlyBase:QuickSearch2017-12-19T16:15:26Z<p>Sian: /* GAL4 etc tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
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===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
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In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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===Controlled Vocabularies===<br />
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Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
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===Auto-completion===<br />
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The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
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Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
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The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
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The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
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In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
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Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000005 qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001761 imaginal disc], but also all terms that have an is_a relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001778 wing disc], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00001768 eye disc]) or part_of relationship (e.g., [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00007111 imaginal disc posterior compartment], [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBbt:00006029 wing pouch]) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/vocabularies Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
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The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Orthologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169440FlyBase:QuickSearch2017-12-19T15:57:09Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) will, in many cases, get around this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169439FlyBase:QuickSearch2017-12-18T23:38:23Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM phenotype ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) resolves this issue.<br />
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The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169438FlyBase:QuickSearch2017-12-18T23:37:21Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
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You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
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You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
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Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
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Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) resolves this issue.<br />
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The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
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The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
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Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
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===Orthologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
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This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
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The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
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The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
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A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
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===Protein Domains tab===<br />
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Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
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===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169437FlyBase:QuickSearch2017-12-18T23:23:38Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) resolves this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169436FlyBase:QuickSearch2017-12-18T23:20:31Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) resolves this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
<br />
Click the 'browse' button to see a full [http://{{flybaseorg}}/lists/FBhh list of Human Disease Model Reports]. This list has been organized as an index, so that you can easily browse to your disease; for example, Machado-Joseph disease is redundantly listed as Machado-Joseph disease, under polyglutamine diseases, and under spinocerebellar ataxia.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169432FlyBase:QuickSearch2017-12-18T23:08:51Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
Please note that disease synonyms work only for exact synonyms that have been attached to a Human Disease Model or to a DO term. So, the search string "ALS" fails to find the disease "amyotrophic lateral sclerosis 4", as "ALS4" is a synonym for that disease, but "ALS" is not. Addition of a wild card (e.g., ALS*) resolves this issue.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
<br />
The results are a hit list of matching Disease Ontology CV terms, Human Disease Model Reports, ''Drosophila melanogaster'' genes associated with a Human Disease Model, and ''Drosophila melanogaster'' alleles with a models_of relationship to a Disease Ontology term. Clicking on the Disease Ontology term of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to Human Disease Model Reports, which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information. Human Disease Model, Gene, and Allele hits take you to the corresponding report.<br />
<br />
<br />
Click the 'browse' button to see a full list of Human Disease Model Reports.<br />
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===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169427FlyBase:QuickSearch2017-12-18T22:29:08Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
Please note that for HGNC and OMIM IDs, you can search only using the digits of the ID number; so 11138 or 606352 work as search terms, but HGNC:11138 or OMIM:606352 do not.<br />
The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms and DOIDs (digits only)<br />
*Human Disease Model names and IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols and IDs<br />
*FlyBase gene symbols, names, and IDs<br />
<br />
<br />
Click the 'browse' button to see a full indexed list of Human Disease Model Reports.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169426FlyBase:QuickSearch2017-12-18T22:17:32Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
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In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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===Controlled Vocabularies===<br />
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Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
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===Auto-completion===<br />
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The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
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Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
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The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
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The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
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In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
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Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene, into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
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You can search by human disease-associated gene using:<br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype symbol (e.g. ALSIN)<br />
*OMIM genotype ID (e.g., 606352)<br />
<br />
You can search ''Drosophila melanogaster'' genes using:<br />
*FlyBase gene symbol (e.g., Sod1)<br />
*FlyBase gene name (e.g., superoxide dismutase 1)<br />
*FlyBase gene ID (e.g., FBgn0003462)<br />
<br />
The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms<br />
*DOIDs (digits only)<br />
*Human Disease Model names<br />
*Human Disease Model IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols<br />
*HGNC IDs<br />
*FlyBase gene symbols<br />
*FlyBase gene names<br />
*FlyBase gene IDs<br />
<br />
Click the 'browse' button to see a full indexed list of Human Disease Model Reports.<br />
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===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169415FlyBase:QuickSearch2017-12-18T21:39:21Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, ''Drosophila melanogaster'' gene, or ''Drosophila melanogaster'' allele into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367 '''or''' 0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene by <br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype ID (e.g., 163890)<br />
The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms<br />
*DOIDs (digits only)<br />
*Human Disease Model names<br />
*Human Disease Model IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols<br />
*HGNC IDs<br />
*FlyBase gene symbols<br />
*FlyBase gene IDs<br />
*FlyBase allele symbols<br />
*FlyBase allele IDs<br />
*FlyBase gene symbols.<br />
<br />
Click the 'browse' button to see a full indexed list of Human Disease Model Reports.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169414FlyBase:QuickSearch2017-12-18T21:33:18Z<p>Sian: /* Human Disease tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
*[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] <br />
*[[FlyBase:QuickSearch#Data Class tab| Data Class tab]]<br />
*[[FlyBase:QuickSearch#Expression tab| Expression tab]]<br />
*[[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]<br />
*[[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] <br />
*[[FlyBase:QuickSearch#GO tab| GO tab]]<br />
*[[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]<br />
*[[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]]<br />
*[[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]]<br />
*[[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]]<br />
*[[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search [https://wiki.flybase.org/wiki/FlyBase:Human_Disease_Model_Report Human Disease Model Reports] and the [http://disease-ontology.org/ Disease Ontology (DO)] by entering a disease, human disease-associated gene, or ''Drosophila melanogaster'' gene into the search box. This search supports a great deal of flexibility in search text. <br />
<br />
You can search by disease using:<br />
*Disease Ontology (DO) term (e.g., autosomal dominant Parkinson Disease 1)<br />
*DOID (e.g., DOID:0060367)<br />
*Human Disease Model name (e.g., Parkinson disease 1)<br />
*Human Disease Model ID (e.g., FBhh0000006)<br />
*[https://omim.org/ OMIM] phenotype term (e.g., PARKINSON DISEASE 1, AUTOSOMAL DOMINANT)<br />
*OMIM ID (e.g., 168601)<br />
*disease synonym (e.g., PD1). <br />
<br />
You can search by human disease-associated gene by <br />
*[https://www.genenames.org HGNC (Human Gene Nomenclature Committee)] gene symbol (e.g., SNCA)<br />
*HGNC ID (e.g., 11138)<br />
*OMIM genotype ID (e.g., 163890)<br />
The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch auto-completion feature is active in this tab; auto-completion works for <br />
*Disease Ontology terms<br />
*DOIDs (digits only)<br />
*Human Disease Model names<br />
*Human Disease Model IDs<br />
*OMIM phenotype terms<br />
*HGNC gene symbols<br />
*HGNC IDs<br />
*FlyBase gene symbols<br />
*FlyBase gene IDs<br />
*FlyBase allele symbols<br />
*FlyBase allele IDs<br />
*FlyBase gene symbols.<br />
<br />
Click the 'browse' button to see a full indexed list of Human Disease Model Reports.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Tools_Overview&diff=169408FlyBase:Tools Overview2017-12-18T20:29:00Z<p>Sian: /* QuickSearch */</p>
<hr />
<div>=General Search Help and Tips=<br />
<br />
FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the 'Tools' drop-down menu in the Navigation bar. In addition to the Navigation bar, which can be accessed from any FlyBase page, the homepage also has direct links to the most commonly used tools.<br />
<br />
Below are brief descriptions of each of the tools, which have been split into five main sections:<br />
<br />
*[[FlyBase:Tools Overview#Overview of Search Strategies|Overview of Search Strategies]] (for example, how to search for expression data) <br />
*[[FlyBase:Tools Overview#Main Query Tools|Main Query Tools]] (Jump to Gene, QueryBuilder, etc.)<br />
*[[FlyBase:Tools Overview#Query Results Analysis Tools|Query Results Analysis Tools]] (Hit list refinement, Batch Download)<br />
*[[FlyBase:Tools Overview#Genomic Search Tools and Browsers|Genomic Search Tools and Browsers]] (GBrowse, BLAST etc.)<br />
*[[FlyBase:Tools Overview#Other Tools|Other Tools]] (Interactions Browser, Find a Person etc.)<br />
<br />
=Overview of Search Strategies=<br />
<br />
==Searching 12 species==<br />
<br />
Please note -- Starting in 2018, FlyBase will reflect updated gene models annotated by the NCBI gnomon pipeline for four species only: D. simulans, D. ananassae, D. pseudoobscura, and D. virilis. Thus, existing gene records for the other seven AAA species may go stale and newly annotated genes will not be included. (D. melanogaster gene models are updated via a separate pipeline.) This section will be updated as these changes occur.<br />
<br />
Individual gene reports for genes from the 12 originally sequenced Drosophila genomes are available in FlyBase. There are four main ways in which these data can be browsed and queried in FlyBase:<br />
<br />
*[http://{{flybaseorg}}/static_pages/downloads/bulkdata7.html Precomputed files]<br />
<br />
*[http://{{flybaseorg}}/blast/ BLAST]<br />
<br />
*[http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse]<br />
<br />
*Gene Report Pages<br />
<br />
For those interested in genome-wide analyses, bioinformatics and comparative genomics, there are a selection of pre-computed files available for download from our precomputed files page (in the Genomes:Annotation and Sequence section, for example), found in the 'Files' menu.<br />
<br />
For those with an interest in a specific gene/protein/region across the different species, there are a number of ways to query the data. Our [http://{{flybaseorg}}/blast/ BLAST server] allows querying of numerous sequenced insect genomes, either individually, as a subset, or all together. Each BLAST hit can then be localised and shown on the genome through [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse]. Orthoview in GBrowse allows movement through the different genomes, illustrating the same region (where possible) in different genomes. In the near future, multiple alignments will be available, enabling direct sequence comparison between the different genomes.<br />
<br />
==Aberrations - deficiencies, dupications, inversions, translocations==<br />
<br />
One of the problems in a field of the size and complexity of Drosophila genetics is the use of nomenclature. This can lead to a number of names being given to the same object, and to the valid FlyBase name or symbol of an object being quite confusing or indeed not in common lab parlance. Aberration naming is no exception. The simplest ways to search for an aberration are either using [http://{{flybaseorg}}/static_pages/cytosearch/cytosearch15.html CytoSearch], when you want to find an aberration that removes a particular gene or uncovers a cytological band, or using [http://{{flybaseorg}}/ QuickSearch] (use the 'Data Class' tab and select 'aberration' as the data class). Remember to use wildcards (i.e. *) to allow for slight differences in naming. FlyBase records all mentions of an aberration, so if an aberration is given a particular symbol in a paper, this name will be recorded as a synonym of the FlyBase 'valid' symbol (see the [http://{{flybaseorg}}/wiki/FlyBase:Nomenclature nomenclature] document for more details). Alternatively, you can browse the molecularly localized aberrations for each chromosome by scanning [http://{{flybaseorg}}/cgi-bin/gbrowse2/dmel/ GBrowse] after selecting all "Aberrations" tracks.<br />
<br />
==Cytologically Mapped Features==<br />
<br />
When looking for cytology, you have a choice of a number of tools on FlyBase, including [http://{{flybaseorg}}/.bin/qbgui.fr.html QueryBuilder]. The easiest tools to use however, are [http://{{flybaseorg}}/static_pages/cytosearch/cytosearch15.html CytoSearch] or [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse]. GBrowse is especially useful when looking for molecularly mapped sequences, insertions, or probes. CytoSearch comes into its own when searching for cytologically defined features, such as cytologically-mapped genes or deficiencies, that haven't been molecularly mapped to the sequence. Of course, as with many aspects of research, complimentary methods should be used. Therefore, we recommend you use both GBrowse and CytoSearch to analyse cytology. <br />
<br />
A description of how FlyBase computes the cytological location for features that have been mapped to the genome can be found in [[FlyBase:Computed cytological data | Computed cytological data]]. Illustrations or electron micrographs of ''D. melanogaster'' polytene chromosomes as well as a cytogenetic-genetic-sequence location correspondence table can be found at [[FlyBase:Maps | ''D. melanogaster'' Chromosome Maps]].<br />
<br />
==Expression Data==<br />
<br />
'''Browsing Expression Data'''<br />
<br />
Expression patterns are captured by FlyBase curators for transcripts, proteins, and "reporters" (i.e. enhancer trap insertions and reporter constructs). Information about transcript and protein expression patterns can be found on gene reports (e.g. the [http://{{flybaseorg}}/reports/FBgn0260400.html elav] gene), data for reporter constructs can be found on recombinant construct reports (e.g. [http://{{flybaseorg}}/reports/FBtp0011922.html P{elav-lacZ.H}]) and associated allele reports (e.g. [http://{{flybaseorg}}/reports/FBal0047660.html Ecol\lacZ<sup>elav.PH</sup>]), and data for enhancer or protein traps can be found on insertion reports (e.g. [http://{{flybaseorg}}/reports/FBti0002575.html P{GawB}elav<sup>C155</sup>]) and associated allele reports (e.g. [http://{{flybaseorg}}/reports/FBal0047071.html Scer\GAL4<sup>elav-C155</sup>]). In all cases, expression data will be found in the "Expression Data" section of the report. For those constructs or insertions that reflect expression of a particular gene, data are also promoted to the corresponding gene report, in a subsection of "Expression Data" labeled "Expression Deduced from Reporters" (e.g. expression data for both [http://{{flybaseorg}}/reports/FBtp0011922.html P{elav-lacZ.H}] and [http://{{flybaseorg}}/reports/FBti0002575.html P{GawB}elav<sup>C155</sup>] are displayed on the [http://{{flybaseorg}}/reports/FBgn0260400.html elav] gene report). Subcellular Localization of protein is populated from [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report#Cellular_Component Gene Ontology (GO) Cellular Component] curation of genes.<br />
<br />
We cooperate with several other databases of expression data and either display a portion of their data within FlyBase (e.g. [http://www.flyexpress.net/ FlyExpress]) and/or link to their database (e.g. [http://fly-fish.ccbr.utoronto.ca/ Fly-FISH]). These types of data can be found in the "External Data & Images" subsection of the "Expression Data" section. Additionally, we maintain a set of links to [http://{{flybaseorg}}/wiki/FlyBase:Images Image Based Resources], including image databases, tools for image analysis, and tools for image visualization and annotation.<br />
<br />
High throughput expression data from [http://flyatlas.org/atlas.cgi FlyAtlas] and [http://www.modencode.org/ modENCODE] can be found on Gene Reports in a subsection of "Expression Data" labeled "High-Throughput Expression Data". The modENCODE data can be visualized as a linear or log graph, or as a heatmap. The FlyAtlas section also includes a 'back-to-back' option, in which gene expression levels in larval tissues are juxtaposed with gene expression levels in the corresponding adult tissues. The graph displays can be scaled by gene maximum expressed, or by low, moderate, or high expression bin max.<br />
<br />
'''Searching for Expression Patterns'''<br />
<br />
Expression data curated from literature can be searched most easily and accurately by using the QuickSearch [http://{{flybaseorg}}/wiki/FlyBase:QuickSearch#Expression_tab Expression] or [http://{{flybaseorg}}/wiki/FlyBase:QuickSearch#GAL4_etc_tab Gal4 etc] tabs (detailed help at links). The Expression tab allows searches for genes by temporal-spatial expression pattern, while the GAL4 etc allows searches for GAL4 and other binary drivers, and non-binary reporters. Another expression pattern search option is [http://{{flybaseorg}}/.bin/qbgui.fr.html QueryBuilder], which supports multipart queries (e.g. generate a list of genes which have the GO term "transcription factor activity" and whose protein products are expressed in the central nervous system). However, if you're interested in all genes expressed in a bodypart, tissue, or developmental stage, you can find that using [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies]. For example, by entering the term "adult mushroom body" into Vocabularies, you can obtain a list of genes expressed in that tissue.<br />
<br />
'''Searching for High-Throughput Expression Patterns'''<br />
<br />
RNA-Seq expression data can be searched to identify genes with specific expression characteristics using the [http://{{flybaseorg}}/static_pages/rna-seq/rna-seq_profile_search.html RNA-Seq Profile Search] tool. Genes that have expression patterns similar to a given gene can be found using the [http://{{flybaseorg}}/static_pages/rna-seq/rna-seq_similarity_search.html RNA-Seq Similarity Search] tool; this search option can also be launched from the relevant gene page. [http://{{flybaseorg}}/static_pages/rna-seq/rnaseqmapper.html RNA-Seq By Region] can be used to compare the RNA-Seq signal for a given region across samples, or to compare signal between two regions within a single sample. For additional information about these tools see the section below, [http://{{flybaseorg}}/wiki/FlyBase:Tools_Overview#RNA-Seq_Tools_and_Browsers RNA-Seq Query Tools and Browsers].<br />
<br />
==Mutant Phenotype Data==<br />
<br />
Mutant phenotype data is associated with alleles in FlyBase, so you need to search allele data if you are interested in mutant phenotype. In addition to free text describing the phenotype, the alleles are indexed with [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase controlled vocabulary] (CV) terms, which makes it easier for you to search for a particular phenotype, e.g. searching for mutants that affect the wing. You can search with these CV terms using either [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] or [http://{{flybaseorg}}/.bin/qbgui.fr.html QueryBuilder].<br />
<br />
You can find mutant alleles affecting the wing from all species using Vocabularies. If you enter the term "wing" into Vocabularies search page and then click on the "Alleles" button in the report page, you will obtain a list of mutant alleles that affect the wing. However, to search in a specific species, or to search for mutant phenotypes as part of a multipart query, QueryBuilder must be used. In this case, you should pick the "CV Hierarchy (GO/etc.)" dataset and then use the term picker to choose the body part, e.g. wing. In both cases, the default is to search both for alleles specifically labelled with the CV term, e.g. wing and also with child CV terms that are a subset of the term chosen, e.g. wing vein. If you want to restrict your search to just the precise term chosen, use QueryBuilder and select 'Retrieve records annotated with "This CV term only"' before you run the query.<br />
<br />
==References==<br />
<br />
FlyBase is an excellent source of Drosophila references. References can be searched in a number of ways. The easiest way is through [http://{{flybaseorg}}/ QuickSearch], on our homepage. Choose the 'References' tab and fill in one or more of the search boxes. The field identity of each search box can be modified using the dropdown menus at the left. For more information, please go to the [http://flybase.org/wiki/FlyBase:QuickSearch QuickSearch Help Page].<br />
<br />
More refined reference searches can be performed using [http://{{flybaseorg}}/.bin/qbgui.fr.html QueryBuilder] (QB). Click on the box titled 'Query is empty.. Click here to start building' on the QB start page to being the search. At this stage the window will be displaying all the fields available to search for the 'Genes' dataset. Change the dataset to 'References'. Now the fields found in the reference reports are displayed. From here, you can search all the data found in the reference report, including pubmed ID, author, and type (e.g. review).<br />
<br />
A popular way to search for references is to search for a (list of) objects (e.g. genes, GO terms) and then to use the 'Show related' toggle on the hits page to change the hit list to the related references. The 'Results Analysis/Refinement' button, found on the hit list page, can be used to analyse the distribution of the references over year, journal, author, and type of publication (e.g. review, paper, abstract).<br />
<br />
==Stocks==<br />
<br />
One of the easiest ways to search for a stock in FlyBase is to use [http://{{flybaseorg}}/ QuickSearch]. Simply change the data class to 'stocks', type in the feature of interest (e.g. a gene symbol, allele symbol), and search. A further way to identify stocks is through the hit list produced after a search. At the top of the hit list there is a toggle allowing you to 'Show related' stocks. Stocks can also be found for individual alleles by clicking on the Stocks matryoska on the allele report page.<br />
<br />
=Main Query Tools=<br />
<br />
==Jump to Gene / Search FlyBase==<br />
Jump to Gene (J2G) and Search Flybase are alternative query tools found in the top-right of the blue navigation bar on every page in FlyBase - these allow for targeted and wide searches of FlyBase, respectively.<br />
<br />
===Jump to Gene===<br />
The J2G mode is a NAVIGATION tool, not a search tool, and thus should be used when you know the name, symbol or ID for your gene/allele, and you simply want to go to the corresponding report page. You can type a gene symbol or synonym, valid gene name, or FBid into the J2G box (e.g. amn, amnesiac or FBgn0086782). This tool also works with FBids for non-gene entities (e.g. FBal0090485 or FBab0002363) and with allele symbols (e.g. amn[X8]).<br />
<br />
J2G searches with your query in the following order:<br /><br />
# primary FlyBase ID (FBgn) any hits? return hit(s), end search<br /><br />
# symbol (case-sensitive) any hits? return hit(s), end search<br /><br />
# symbol (case-insensitive) any hits? return hit(s), end search<br /><br />
# synonym (case-sensitive) any hits? return hit(s), end search<br /><br />
# synonym (case-insensitive) any hits? return hit(s), end search<br /><br />
# name (case-sensitive) any hits? return hit(s), end search<br /><br />
# secondary FlyBase ID any hits? return hit(s), end search<br /><br />
<br />
If nothing found, return error page<br />
<br />
J2G searches D. melanogaster genes by default. If you would like to search for a non-melanogaster gene, you need to use the unique, 4-letter species abbreviation, followed by a backslash, and then the gene symbol (e.g. Dpse\dpp), or use the respective FBgn identifier.<br />
J2G does NOT search name synonyms!<br />
J2G entries allow wildcards (*), but non-unique results may be returned.<br />
<br />
===Search FlyBase===<br />
The Search FlyBase mode is the same as the [http://{{flybaseorg}}/ QuickSearch - Search FlyBase] tab found at the HomePage. It performs a comprehensive search of text-searchable FlyBase data across all classes of reports and the results are displayed in the form a Hit List summarizing the matching records by data type. For example, a search for 'amn' retrieves the matching reports for Aberration, Allele, Anatomy Ontology, Clone, Dataset, Gene, etc...<br />
<br />
By clicking on one or more of the data types in the hit list it will only display individual matches within those data types. Click on any of the individual hits to view the corresponding report page.<br />
<br />
'Search FlyBase' entries allow wildcards (*) to broaden the query. 'Search FlyBase' entries also allow multiple terms: a Boolean 'AND' is used as default (e.g. ‘cnn cbs’ equals to 'cnn AND cbs'). Adding 'OR' between terms will find records that have one or another of a list of terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, use the ‘-’ character as a prefix (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
==QuickSearch==<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching across all data types or for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Use the "Simple" tab to search all FlyBase reports. Results are in the form of a hit list summarizing the matching records by data type. More limited searches are available in the remaining tabs. You can search for particular curated data classes, e.g. genes, alleles, aberrations, etc. (Data Class tab), Human Disease models (Human Disease tab), Orthologs (Orthologs tab), GAL4 and other drivers and reporters (GAL4 etc tab), Protein Domains (Protein Domains tab), Gene Expression (Expression tab), Gene Groups (Gene Groups tab), Phenotype (Phenotype tab), Gene Ontolgy (GO tab), and References (References tab).<br />
<br />
QuickSearch searches ''D. melanogaster'' data by default. The "Simple, Expression, and "Data Class" tabs offer the option to search all species. If you want to search for a gene in a particular species, you can use the unique, 4-letter [[FlyBase:Abbreviations | species abbreviation]], followed by a backslash, and then the gene symbol (e.g. Dpse\dpp).<br />
<br />
For a full description of the QuickSearch tabs, see [https://wiki.flybase.org/wiki/FlyBase:QuickSearch QuickSearch Help Page].<br />
<br />
==QueryBuilder==<br />
<br />
[http://{{flybaseorg}}/.bin/qbgui.fr.html QueryBuilder] (QB) provides the most powerful way to search FlyBase on a field-by-field level. QB presents a simple user interface that supports powerful searches by offering access to DataSet|Field pairs (for example, Genes|CV:GO:Molecular Function) in FlyBase along with the ability to include any combination of datasets in the same search (Note that Human Disease, Cell Line, Gene Group, and Strain reports are not yet accessible with QueryBuilder). QB automatically creates sets of records that are cross-referenced to the records that match your query, providing links to all related records in FlyBase from a single page. Both simple and complex queries can be built in a few steps. A search can be focused on a particular piece of data within a report page, such as the 'mapped features and mutations' associated with a gene, and Boolean operators (and, or, but not) can be used to combine two or more searches. QB allows a user to perform much more sophisticated searches compared to [http://{{flybaseorg}}/ QuickSearch] or other search tools on FlyBase, by taking full advantage of how the data is stored in FlyBase. A useful feature of QueryBuilder is that sets of results can be exported to QB from hitlists, as described in the 'Hit list refinement' section, and then modified to refine the search by adding additional query segments. Thus, QB is a very powerful tool that can be used in many different ways to explore the data in FlyBase.<br />
<br />
The 'Query Builder Help' section on the '[http://{{flybaseorg}}http://beta.flybase.org/cgi-bin/qb.pl QueryBuilder Home Page]' outlines the basic search strategy. There are three options on the QB start page: select a pre-constructed query, import a previously saved query, and build a new query. Help for all of these options is available further down the page as well as a description of how to carry out an expression data search.<br />
<br />
==Vocabularies (previously known as TermLink)==<br />
The [http://{{flybaseorg}}vocabularies Vocabularies Search Page] provides easy access to data annotated with a particular controlled term or one of its synonyms. For example, you can use Vocabularies to retrieve a list of all the genes annotated with a particular GO term, or all the transcripts expressed in a particular body part. You do not need to know the precise term that FlyBase uses to store the data; the search box on the Vocabularies page retrieves controlled vocabulary terms that contain your query or terms that list a synonym containing the search term. For example, if you enter wing you will obtain a list that includes the controlled terms wing, anterior wing margin, and dorsal mesothoracic disc, which has the synonym wing disc. The controlled terms in the list are hyperlinked to TermReport pages that describe a single term in detail. Alternatively, you can also browse various controlled vocabulary hierarchies, by using the trees displayed on the main Vocabularies page.<br />
<br />
The [http://{{flybaseorg}}vocabularies Vocabularies Search] is the only search tool in FlyBase that allows users to search directly for controlled vocabulary (CV) term reports from any of the controlled vocabularies (CVs) used by FlyBase. This includes the GO and anatomy hierarchies, among others. Wildcards are automatically added to the beginning and the end of a search term. For each search performed, Vocabularies returns a hit list of CV term reports that match the search term. These are listed according to CV type, in the following order: anatomy term reports, FlyBase controlled vocabulary term reports, development term reports, GO term reports and SO term reports. Each term report allows the user to retrieve gene, allele, transcript, polypeptide or image reports associated with the term.<br />
<br />
Please go to [[FlyBase:Vocabularies | Vocabularies Help]] for more information. This page can also be accessed from the bottom of the [http://{{flybaseorg}}vocabularies Vocabularies Search Page].<br />
<br />
There is a [https://www.youtube.com/watch?v=jgCON15SiRo video tutorial] on YouTube.<br />
<br />
=Query Results Analysis Tools=<br />
==HitList Refinement==<br />
When you perform any search that returns multiple hits, you are presented with a hit list, that can be modified or refined. By default all records are selected for inclusion in subsequent manipulations, but the checkboxes allow user-defined subsets to be created. The first data column links directly to the report for each record that matched your search. Other columns link to [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] or to searches that return hits directly related to that record. In addition to these links, the hit list provides a set of powerful tools for query refinement or batch processing.<br />
<br />
The 'Show related' drop down menu enables you to see all objects of a particular class that are related to the hits selected in your list. For example, selecting 'clones' from the 'Show related' menu of a gene search will return a list of clones that are related to the selected genes.<br />
<br />
The 'Results Analysis/Refinement' button allows you to see the frequency of values within your selected hits for a predefined list of fields. Selecting 'Biological process', for example, from the Results Analysis/Refinement tool for a list of genes involved in the Notch signalling pathway will result in a page listing the distribution of the different biological process controlled vocabulary terms associated with the list. Clicking on the number in the 'Related records' column will return the genes from your hitlist that are annotated to be involved in that GO term.<br />
<br />
Lastly, the 'HitList Conversion Tools' button allows you to send the selected hits to our Batch Download tool for use offline, to a new QueryBuilder session for further querying, or to link-out HTML tables of various third party data sources with data linked to the hits in your result list.<br />
<br />
==Batch Download==<br />
The [http://{{flybaseorg}}/static_pages/downloads/ID.html Batch Download] tool provides bulk access to a variety of data and data formats, such as FASTA sequence data and XML files, for a specified list of unique IDs (please note: secondary IDs, synonyms, or full names are not allowed because they are not unique).<br />
<br />
IDs can be sent from a FlyBase hit list, uploaded from a local file, or entered manually.<br />
<br />
The Field Data output format provides access to two types of data: data from our set of precomputed flat files and data from the HTML reports. Any line from a precomputed file that matches the lists of IDs supplied can be downloaded using the precomputed file option.<br />
<br />
The HTML table option allows you to create a custom report with only the fields you want while preserving hyperlinks for direct navigation to other FlyBase data. Recently the HTML table option has been improved by listing all fields as they appear on the report pages, and making them easier to identify by categorising them as CV (controlled vocabulary), Symbol, Date, or Text.<br />
<br />
=Genomic Search Tools and Browsers=<br />
<br />
==BLAST==<br />
[http://{{flybaseorg}}/blast/ BLAST] (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases. FlyBase BLAST allows the opportunity to BLAST query the 12 completed Drosophila genomes, along with related insect species for which full genomes have been sequenced. BLAST provides access to the FASTA sequences of all sequenced Drosophila sequences, as well as providing links to GenBank. In addition, you can BLAST an unknown sequence and identify its position on GBrowse.<br />
<br />
The [http://{{flybaseorg}}/blast/ BLAST] homepage is split into three sections; the first allows the user to input the query sequence and set-up the standard BLAST parameters (e.g. Expectation value, database to be searched); the second section allows the species to be selected; while the third allows the user to specify advanced BLAST options.<br />
<br />
Clicking on the hyperlinks provides hints and tips for the BLAST search.<br />
<br />
==GBrowse==<br />
FlyBase [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] provides a graphical or tabular representation of the 12 sequenced Drosophila genomes. Genes, insertions, deficiencies, mapped mutations, RNA-seq data, orthologous regions in other Drosophila genomes, and a wide array of other mapped features can be selected and viewed along a genome coordinate scale. <br />
You can navigate to a specific location by entering a precise sequence range, any valid FlyBase identifier for a gene, gene product, or insertion, or a cytological band in the 'Landmark or Region' box. Additionally, FlyBase BLAST output includes GBrowse links that display each BLAST alignment as a highlighted feature in the context of neighbouring gene models and other features of the region.<br />
<br />
By default FlyBase presents a view of D.melanogaster that displays gene models, transcripts, natural transposon insertion sites, repeat regions, estimated cytological bands, cDNAs, transgenic insertion sites, Gnomon gene predictions, regions with orthologs in other drosophila species and the modENCODE Developmental stage RNA-seq track. Tracks can be easily reordered by clicking on the track name and dragging to a new location on the viewer. Additional tracks can be selected from the 'Select Tracks' link at the top of the Browser. Descriptions of individual tracks can be accessed from the "?" icon next to each track on the 'Select 'tracks' page or at the [http://{{flybaseorg}}/wiki/FlyBase:GBrowse_Tracks GBrowse tracks document at the FlyBase wiki]. A set of icons next to the track names in the GBrowse viewer provide options for managing tracks including the option to show, hide, turn off, get information about and configure each track. The configure tracks options for the RNA-seq expression tracks are particularly helpful, including the ability to choose a log2 or linear view and track spacing; see description at [http://{{flybaseorg}}/static_pages/feature/previous/articles/2014_11/topoview_config.html Custom configurations of RNA-Seq profiles in GBrowse]. Together, these options allow a highly customized view of the data.<br />
<br />
See the [[FlyBase:GBrowse|FlyBase GBrowse Help]] wiki page for FlyBase-specific tips (there is also a link at the top right of the GBrowse window). A more generic GBrowse help manual, [http://{{flybaseorg}}/.gb2/general_help.html 'Help with this browser'], provides additional details on other very useful features of the GBrowse viewer, and can be accessed from the Help menu in the upper right corner of the GBrowse page. Additional representations of the genome data including a tabular view of mapped features or decorated FASTA can be selected and configured from the drop down menu in the upper right corner of the viewer.<br />
<br />
===Finding orthologs using GBrowse===<br />
<br />
By adding 'Similarity' tracks to the D.melanogaster genome view you can use the resulting ortholog links to navigate to orthologs in the other species. You can also find an ortholog by selecting the species from the 'Data Source' menu and entering the D.melanogaster gene symbol or FBgn ID in the 'Landmark or Region' box. In addition, as described above, FlyBase BLAST output provides links to GBrowse. This is an extremely useful entry path into the sequence data of species other than D.melanogaster, which in some cases is comprised of a large number of relatively short unlinked scaffolds.<br />
<br />
==JBrowse==<br />
FlyBase [http://{{flybaseorg}}/cgi-bin/jbrowse/dmel/ JBrowse] provides a graphical representation of the Drosophila melanogaster genome. JBrowse was developed by the Generic Model Organism Database ([http://gmod.org/wiki/Main_Page GMOD]) consortium to be the eventual successor to GBrowse. It is offered in FlyBase in parallel to GBrowse2 until all the features now available in GBrowse2 can be made available in JBrowse. <br />
<br />
Genes, cDNAs, insertions, deficiencies, mapped mutations, regulatory features, RNAi reagents, RNA-seq data, and a wide array of other mapped features can be selected and viewed along a genome coordinate scale. You can navigate to a specific location by entering a precise sequence range, any valid FlyBase identifier for a gene, gene product, or insertion, or a cytological band in the 'Landmark or Region' box. Then move laterally along the genome by using the arrows at the top of the browser or by clicking in an open area of the viewer and dragging side to side. You can zoom in and out by clicking the plus and minus icons in the navigation bar or zoom in by selecting a region of the lower coordinate scale. You can move to a different region of the chromosome arm by clicking on a spot on the chromosome scale at the top of the viewer and switch to a different chromosome by using the chromosome selector at the top. <br />
<br />
FlyBase presents a view of D.melanogaster that displays gene models and the modENCODE Developmental stage RNA-seq track. Additional tracks can be selected from the 'Available Tracks' menu at the left side of the Browser. Tracks can be easily reordered by clicking on the track name and dragging to a new location on the viewer. Descriptions of individual tracks can be found in the [[FlyBase:JBrowse Tracks|FlyBase JBrowse Tracks]] document at the FlyBase wiki]].<br />
<br />
See the [[FlyBase:JBrowse|FlyBase JBrowse Help]] wiki page for FlyBase-specific tips. More generic JBrowse help can be accessed from the Help menu in the upper row of the JBrowse page.<br />
<br />
==Chromosome Maps==<br />
The [http://{{flybaseorg}}/maps/chromosomes/maps.html chromosome maps] show sequence scaffolds aligned to polytene chromosome maps for the Muller elements of the sequenced Drosophila species. For more information on the syntenic relationships among the 12 sequenced genomes, their standard chromosomal numbering and corresponding Muller element please see the [http://{{flybaseorg}}/maps/chromosomes/synteny_table.html Muller Element Arm Synteny] Table. The aligned sequence scaffolds, shown in blue on the maps, provide access to the sequence data and gene models. When you move your cursor over one of the blue scaffolds a yellow box appears that corresponds to a GBrowse window, and clicking on the box will take you to the corresponding location in GBrowse.<br />
<br />
==CytoSearch==<br />
[http://{{flybaseorg}}/static_pages/cytosearch/cytosearch15.html CytoSearch] lists are regional maps of the ''Drosophila melanogaster'' genome incorporating both sequence-based and cytology-based map data. Sequence-based data trumps cytology when both are available, cytology trumps meiotic data when both are available, and estimated cytology is used when only meiotic data are available. The FlyBase [http://flybase.org/w/images/a/a2/DmelMapTable.xlsx correspondence table] for cytological and sequence level maps are used to estimate cytology from sequence range and sequence range from cytology, for both the underlying data and the query input.<br />
<br />
CytoSearch is useful for searching for genetic objects mapped to a particular genomic region (but not necessarily mapped to the sequence).<br />
<br />
==Coordinate Converter==<br />
The [http://{{flybaseorg}}/convert/coordinates Coordinate Converter] allows you to convert genomic coordinates between different genome releases. Just select the species, the input and output assemblies, enter your list of coordinates (or load them from a file), and away you go! It's that simple. The output page or file will list the input coordinates (with the release), the output coordinates (with the release), and Notes on the conversion (e.g., "includes 1 area of change; different scaffold"). See [[FlyBase:Coordinate_Converter | Coordinate Converter]] help page for more information.<br />
<br />
==Feature Mapper==<br />
The [http://{{flybaseorg}}/static_pages/featuremapper/featuremapper.html Feature Mapper] tool allows you to do a search with one or many genes, sequence-based features or genomic regions and returns a wide variety of sequence-based genomic features that overlap or map within the associated genomic region(s). The reported features include gene structure features, aligned evidence, noncoding features, mapped mutations, and RNAi reagents. The search returns lists of features that map to the region(s) of interest. Enter the symbols or IDs for genomic features or a sequence region, check the features that you wish to have returned, and submit your query. Search results can be saved as a GFF file or exported to a hitlist. For more information, see [[FlyBase:Feature Mapper | Feature Mapper]]<br />
<br />
=RNA-Seq Query Tools and Browsers=<br />
<br />
The primary RNA-Seq data in FlyBase are the modENCODE data originally published in [http://{{flybaseorg}}/reports/FBrf0213330.html Graveley et al., 2011] and [http://{{flybaseorg}}/reports/FBrf0225793.html Brown et al., 2014], comprising 30 developmental stage expression profiles, 29 tissue expression profiles, 25 treatment/condition expression profiles and 24 cell line expression profiles. RNA-Seq reads were mapped to the Release 6 genome assembly as described in [http://{{flybaseorg}}/reports/FBrf0226107.html Brown et al., 2014]. In GBrowse genomic views, several other RNA-Seq datasets are also presented. The RNA-Seq query tools are restricted to the modENCODE datasets. For each modENCODE RNA-Seq sample, gene expression level was calculated as RPKM within the exonic extent of the gene, as described in [http://{{flybaseorg}}/reports/FBrf0221009.html Gelbart and Emmert, 2013]. For purposes of presentation and queries, values were assigned to one of eight bins, from very low to extremely high.<br />
<br />
There is direct link from the FlyBase home page (top array of icons) to an [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq] overview page that includes the tools and options described below.<br />
<br />
==GBrowse/JBrowse==<br />
<br />
FlyBase [http://{{flybaseorg}}/cgi-bin/gbrowse/dmel/ GBrowse] has several tracks that display RNA-Seq expression profiles, which give coverage values base-by-base across the genome. Choose datasets for expression by stage, tissue, treatments, or cell lines. By default, the many tracks are displayed in the layered FlyBase “TopoView” format, and data are shown on a log2 scale, since they range over many orders of magnitude. There are many customization options, including using a linear scale, viewing a subset of tracks within an RNA-Seq dataset, and removing the view offset; details are provided [http://{{flybaseorg}}/static_pages/feature/previous/articles/2014_11/topoview_config.html here]. Currently, the RNA-Seq data presentation in FlyBase JBrowse is more limited (restricted to the modENCODE developmental stages) and cannot be customized.<br />
<br />
==RNA-Seq Profile==<br />
[http://{{flybaseorg}}/static_pages/rna-seq/rna-seq_profile_search.html RNA-Seq Profile] is a fine grained query tool, powered by modENCODE high-throughput RNA-Seq expression data, that allows you to find genes with specific patterns of expression across several variables. Interested in development of the central nervous system? Search for genes that are expressed in these tissues during a specific developmental stage. Curious how toxins affect the fly reproductive system? Search for genes expressed in fly gonads that are activated (or suppressed) by exposure to Paraquat or Rotenone. <br />
<br />
Choose datasets for expression by stage, tissue, treatments, or cell lines, or use several datasets in conjunction. Each dataset is presented in a form that allows you to select either narrow slices of the data, or larger sections for more coverage. You also have control over the levels of expression used in the search, allowing you to define distinct thresholds for the ON and OFF states. Keep in mind that extremely narrow search conditions may produce sparse or empty result sets. Feel free to experiment; the tool will remember your settings so that you can adjust, instead of needing to re-enter them. Search results can be exported, as usual, for further analysis or download.<br />
<br />
NB: The group check box selectors are interpreted differently depending on whether you are making selections from the 'Expression ON' or 'Expression OFF' sections. <br />
'Expression ON' selectors: Selecting multiple stages using one of the grouping check boxes acts as an 'OR'. This means that if a gene is expressed at or above the chosen expression level in any one or more of the selected stages it will be returned in the result list. To get 'AND' behavior (i.e., return only those genes which are expressed at the chosen level in each one of the selected stages) you must select each of the stages individually. <br />
'Expression OFF' selectors: Selecting multiple stages using one of the grouping check boxes acts as an 'AND'. This means that for a gene to be returned in the result list, the observed level of expression must be at or below the selected level in all of the selected group stages. Therefore, for the 'expression OFF' selectors, checking a group check box is functionally identical to selecting each individual sub-category.<br />
<br />
==RNA-Seq Similarity==<br />
[http://{{flybaseorg}}/static_pages/rna-seq/rna-seq_similarity_search.html RNA-Seq Similarity] finds genes with expression patterns that are similar to that of a given gene; this search option can also be launched from the relevant gene page. 'Similar to' in this case means that the pattern of higher and lower expression<sup>1</sup> in the categories for the RNA-Seq expression experiment data you choose are close to those of your chosen gene, as measured by the correlation coefficient<sup>2</sup> between the data for your given gene and each of the search result genes. Enter your query gene symbol in the box, and choose to search for genes with similar expression by developmental stage, tissue, treatments, or cell lines. You can also specify a subset of experimental samples within a set of RNA-Seq expression data to use when making comparisons. The resulting genes can be exported to a FlyBase hit list.<br />
<br />
<sup>1</sup> Note that two expression patterns will be flagged as similar if the profile of peaks and troughs of expression have a similar shape, even though one expression pattern may have much higher or lower values overall.<br />
<br />
<sup>2</sup> FlyBase uses a generalized Spearman rank correlation for this statistic.<br />
<br />
==RNA-Seq By Region==<br />
[http://{{flybaseorg}}/static_pages/rna-seq/rnaseqmapper.html RNA-Seq By Region] can be used to compare the RNA-Seq signal for a given region across samples, or to compare signal between two regions within a single sample.<br />
<br />
Supply the symbol or FBgn ID for one gene of interest, and choose to query either the developmental or tissue RNA-Seq profiles. The tool will retrieve the locations of all exons for the gene specified, and report an average RNA-Seq signal for each region. Values are normalized for read depth across a given set, and reported as values from 1 to 50; very high read values are truncated at a value of 50. Alternatively, input one or more genomic regions using standard GBrowse coordinate nomenclature (e.g., X:350000..351000) and the tool will return the average RNA-Seq signal for each submitted genomic span; for multiple regions, enter one region per line in the input box.<br />
<br />
For fast visual inspection of the potentially large expression tables, the background of table cells is colored in the same way as in the heatmap coloring schema of expression histograms in FlyBase gene reports. These tables can be copied and downloaded and used for further analysis.<br />
<br />
Note that the signal reported for a given region may arise from the expression of multiple transcripts from one or more genes; the tool simply reports the total signal for that region and does not attempt to assign the expression in that region to any specific transcript.<br />
<br />
=Other Tools=<br />
<br />
==Google<sup>TM</sup> FlyBase==<br />
We have a [http://{{flybaseorg}}/static_pages/search/site_search.html Google search box] (found in box the Tools and Help menus) that can be used to search the entire FlyBase site in a Google-style manner. Google FlyBase is best used to search documentation, but not necessarily to search data about a gene, as it does not restrict its search to specific data fields, and results depend upon Google indexing which cannot be controlled by FlyBase (i.e. you may not find results specific to the newest release).<br />
<br />
==Interactions Browser==<br />
The [http://{{flybaseorg}}/cgi-bin/get_interactions.html Interactions Browser], accessible under the 'Tools' menu or at the top of the Interaction section of allele reports, provides a graphical way of exploring the genetic interaction data (enhancer data only, suppressor data only, or both). The browser works in two modes: You can either search for the interactions of an allele, or the interactions of a gene. The latter will show the interactions of all alleles of the gene. Each node of an interaction diagram is a hyperlink, which enables you to navigate and browse the complex web of known genetic interactions. Placing your cursor over the center of a node activates a pop-up window that in the case of a network of gene interactions contains a summary of the function of that particular gene, while in the case of interactions between alleles shows the context in which the interactions of that allele have been reported. For more information, go to the [http://{{flybaseorg}}/static_pages/newhelp/interactions_browser_help.html Interactions Browser help documentation].<br />
<br />
==ImageBrowse==<br />
[http://{{flybaseorg}}/static_pages/imagebrowser/imagebrowser10.html ImageBrowse] allows the user to browse through [http://{{flybaseorg}}/static_pages/newhelp/image_help.html image reports] by organ system, life-cycle, tagma, or germ layer, as well as to browse images of different Drosophilids. This section also gives access to [http://{{flybaseorg}}/cgi-bin/get_static_page.pl?file=posters.html&title=Contributed%20Posters posters of common visible markers in D. melanogaster], as well as miscellaneous images and quick-time films. [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase Controlled vocabulary terms] are used to annotate and label the images. To search images, and to link relevant gene, allele, transcript and protein records to stages of development, a region of the body or to a specific body part, go to [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies].<br />
<br />
==Find a Person==<br />
FlyBase compiles Drosophila Researcher information to aid networking and communication in the community. To add yourself to the database, use the [http://{{flybaseorg}}/static_pages/people/fbpeopleadd3.html Add a new Person tool], found in the Tools menu.<br />
<br />
[http://{{flybaseorg}}/static_pages/people/people_query6.html Find a Person] allows you to select which field of the personal data you want to search. For example, to search for all the registered Drosophila Researchers in a particular city, you can select the city field and search for the city of interest.<br />
<br />
Simple combinatorial searches are also possible, for example you can search for 'Smith' in 'Texas', if you so desire.<br />
<br />
The search can also be to Principal Investigators (PIs) by ticking the 'Search for PIs only' box.<br />
<br />
==Update an Address==<br />
<br />
To [http://{{flybaseorg}}/static_pages/people/fbpeopleup.html update an existing address], the name of the person concerned should be typed into the text box. If the name is ambiguous, e.g. Smith, then a list of full names containing the name is provided.<br />
<br />
From here, clicking on the name to change allows the details to be altered. A confirmation e-mail will be sent to the given e-mail address to confirm the changes.<br />
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[[Category:FlyBase]] [[Category:Help]]</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169195FlyBase:QuickSearch2017-12-13T22:12:06Z<p>Sian: /* GAL4 etc tab */</p>
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<div>==General help==<br />
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===Overview===<br />
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The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
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Links to specific help for each tab:<br />
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[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] |[[FlyBase:QuickSearch#Data Class tab| Data Class tab]] | [[FlyBase:QuickSearch#Expression tab| Expression tab]] | [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]] | [[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] | [[FlyBase:QuickSearch#GO tab| GO tab]] | [[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]] | [[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]] | [[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]] | [[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]] | [[FlyBase:QuickSearch#References tab| References tab]]<br />
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Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
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===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
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In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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===Controlled Vocabularies===<br />
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Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
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===Auto-completion===<br />
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The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
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Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
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The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Coordinated Auto-completion===<br />
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The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
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In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
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Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
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===Wild Cards===<br />
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When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
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'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
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==Tab Descriptions==<br />
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===Search FlyBase tab===<br />
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This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
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Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
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Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
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===Data Class tab===<br />
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The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
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Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
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Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
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Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
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If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
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'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
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===Expression tab===<br />
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Search for genes according to expression patterns:<br />
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The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
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You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
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The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
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===GAL4 etc tab===<br />
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The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
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'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
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'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
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'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
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'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier]terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000322 pair rule expression pattern] are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
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'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
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'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
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===Gene Groups tab===<br />
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This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
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To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
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Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
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===GO tab===<br />
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Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
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Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
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===Human Disease tab===<br />
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Search the [http://disease-ontology.org/ Disease Ontology (DO)] by entering the name of a disease into the search box. The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
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The QuickSearch auto-completion feature is active in this tab.<br />
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Click the 'browse' button to see a full list of Human Disease Model Reports.<br />
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===Orthologs tab===<br />
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This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
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To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
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The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
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Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
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On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
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In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
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Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
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For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
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===Phenotype tab===<br />
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This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:QuickSearch&diff=169190FlyBase:QuickSearch2017-12-13T21:44:34Z<p>Sian: /* Expression tab */</p>
<hr />
<div>==General help==<br />
<br />
===Overview===<br />
<br />
The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.<br />
<br />
Links to specific help for each tab:<br />
<br />
[[FlyBase:QuickSearch#Search FlyBase tab| Search FlyBase tab]] |[[FlyBase:QuickSearch#Data Class tab| Data Class tab]] | [[FlyBase:QuickSearch#Expression tab| Expression tab]] | [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]] | [[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] | [[FlyBase:QuickSearch#GO tab| GO tab]] | [[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]] | [[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]] | [[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]] | [[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]] | [[FlyBase:QuickSearch#References tab| References tab]]<br />
<br />
Also see this publication:<br />
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)<br />
: '''Exploring FlyBase Data Using QuickSearch.'''<br />
: [http://dx.doi.org/10.1002/cpbi.19 Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23] [http://{{flybaseorg}}/reports/FBrf0234167.html (FBrf0234167)]<br />
<br />
===Species Searched===<br />
The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.<br />
<br />
In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
===Controlled Vocabularies===<br />
<br />
Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "[http://flybase.org/static_pages/termlink/termlink.html Vocabularies]" button above the QuickSearch box on the home page.<br />
<br />
===Auto-completion===<br />
<br />
The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.<br />
<br />
Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.<br />
<br />
The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Coordinated Auto-completion===<br />
<br />
The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:<br />
<br />
In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.<br />
<br />
Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.<br />
<br />
===Wild Cards===<br />
<br />
When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.<br />
<br />
'''Please note''' that wild cards cannot be used in numeric fields (year, ''etc'').<br />
<br />
==Tab Descriptions==<br />
<br />
===Search FlyBase tab===<br />
<br />
This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. Choose whether to limit the search to D. melanogaster records (the default) or to include additional organisms by checking the ‘include non-Dmel species’ box. <br />
<br />
Enter one or more search terms in the box. The search term box of the Simple tab supports a number of additional features that can be used to narrow or broaden the query. A wildcard character (*) can be appended, prepended or added within a search term to broaden the query. When specifying multiple terms, a Boolean ‘AND’ is used for searches by default and does not require any special notation (e.g. a search for ‘neurogenesis microtubule polymerization’ will return only hits that have all of those three terms somewhere in the record). A Boolean ‘OR’ can be added to find records that have one or another of a list of specified terms (e.g. ‘cnn OR cbs’). To exclude certain terms from the results, prefix the term(s) to be excluded with a ‘-’ character (e.g. ‘Parkinson -CG5680’). Finally, results can be specified to contain an exact phrase by surrounding the search term with double quotes (e.g. “SH3 domain”).<br />
<br />
Click on the 'Search' button or press 'enter'. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. Click on any of these to view its report page. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is not active in this tab.<br />
<br />
===Data Class tab===<br />
<br />
The Data Class tab allows searches that are restricted to only a single chosen data type.<br />
<br />
Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.<br />
<br />
Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.<br />
<br />
Enter a symbol appropriate to the selected data type in the "Enter text" box. <br />
Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.<br />
<br />
If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.<br />
<br />
'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.<br />
<br />
===Expression tab===<br />
<br />
Search for genes according to expression patterns:<br />
<br />
The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well as expression associated with reporter constructs and insertions. Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy/Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. You do not need to fill every box to search.<br />
<br />
You can refine this search further by choosing to add [http://{{flybaseorg}}/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the "'''+'''" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Developmental Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component.''' qualifier fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.<br />
If you are looking for expression patterns of GAL4 or other binary drivers or lacZ or GFP reporters, use the new [[FlyBase:QuickSearch#GAL4 etc tab| GAL4 etc tab]]. Alternatively, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.<br />
<br />
The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the [http://{{flybaseorg}}/static_pages/rna-seq/RNA-Seq.html RNA-Seq overview page] at the bottom of the tab to get a more detailed description of these RNA-Seq search options.<br />
<br />
===GAL4 etc tab===<br />
<br />
The GAL4 etc tab allows searches for GAL4 and other binary system drivers, and for non-binary reporters, by temporal-spatial expression pattern as curated from the literature.<br />
<br />
'''Driver/Reporter''' Choose from among five '''Driver/Reporter''' options: GAL4, QF, or LexA binary drivers, or lacZ or GFP reporters.<br />
<br />
'''Output format options''' Choose the '''Output format''': Integrated Table or List. The List output, available only on FlyBase 2.0, provides a faceted hitlist consisting of alleles, insertions, transgenic constructs, and stocks. The Integrated Table output, available on both the main FlyBase website and on FlyBase 2.0, provides a customized table view of the hitlist. This format shows the connection between particular alleles, insertions, constructs, and stocks; additionally, the '''Relevant Expression Statements''' column lists the anatomy, stage, and/or GO cellular component [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] term that triggered the search result. The Integrated Table view also pre-sorts drivers/reporters with a publically available stock to the top of the hitlist.<br />
<br />
'''Search by expression pattern''' Choose the expression pattern you wish to search for. The form has input boxes for '''Developmental Stage''', '''Anatomy or Cell Type''', and '''Cellular Component'''. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled. <br />
<br />
'''Search with qualifier terms ''' You can refine this search further by choosing to add [http://flybase.org/.bin/cvreport.html?cvterm=FBcv:0000052+childdepth=2+rel=is_a qualifier] terms. Click the “'''+'''” sign above the search boxes to bring up additional search boxes for entering qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the '''Stage''' input will affect which qualifier terms are suggested for the '''Anatomy/Cell Type''' or '''Cellular Component qualifier''' fields. Please note: many embryonic expression patterns, such as "pair rule expression pattern" are spatial qualifiers, not anatomy terms; you can search for such terms by filling the '''Anatomy/Cell Type qualifier''' box while leaving the '''Anatomy/Cell Type''' box unfilled.<br />
<br />
'''Choosing the correct search stringency''' It is important to note that you should fill only as many fields as you need; for this tab, you should usually leave the '''Cellular Component''' field unfilled. Also note that this tool supports searching a set of hierarchical controlled vocabularies. For example, if you search '''GAL4 drivers''' for the anatomy term "imaginal disc", you will get not only the list of all such drivers annotated with the term "imaginal disc", but also all terms that have an is_a relationship (e.g., wing disc, eye disc) or part_of relationship (e.g., imaginal disc posterior compartment or wing pouch) to "imaginal disc". The terms that appear in the '''Relevant Expression Pattern''' column of the Integrated Table hitlist can assist you in choosing a more specific search term; you can also use the [http://flybase.org/static_pages/termlink/termlink.html Vocabularies] tool to find controlled vocabulary terms. <br />
<br />
'''Accessing the full expression pattern''' Note: Many drivers and reporters may be expressed at other developmental stages and/or in other tissues or cell types than the pattern you searched for; clicking through to the '''Insertion Reports''' or '''Construct Reports''' of your hits will allow you to see the complete curated expression pattern of the drivers or reporters in your hitlist.<br />
<br />
===Gene Groups tab===<br />
<br />
This tab searches FlyBase-curated 'Gene Groups' - sets of genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. cadherins or caspases).<br />
<br />
To use, either start typing and select the appropriate Gene Group name from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions, or enter your own text, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Then click the 'Search' button or press 'enter'. The resulting hits will be Gene Groups that wholly or partially match your search term. Alternatively, enter the symbol, name or ID of a gene in the search box to retrieve those Gene Groups to which that gene belongs.<br />
<br />
Click the 'browse' link at the bottom of the panel to see a full list of Gene Groups.<br />
<br />
===GO tab===<br />
<br />
Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.<br />
<br />
Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.<br />
<br />
===Human Disease tab===<br />
<br />
Search the [http://disease-ontology.org/ Disease Ontology (DO)] by entering the name of a disease into the search box. The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.<br />
<br />
The QuickSearch auto-completion feature is active in this tab.<br />
<br />
Click the 'browse' button to see a full list of Human Disease Model Reports.<br />
<br />
===Orthologs tab===<br />
<br />
This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for humans and 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~50 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.<br />
<br />
To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes'''. Where the input species is ''D. melanogaster'', there is a choice between searching for orthologs in 'humans and model organisms' (the DIOPT dataset) or in 'Drosophila species, insects etc' (the OrthoDB dataset). Finally, click the '''Search''' button or press ‘enter’.<br />
<br />
The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:<br />
{| class="wikitable"<br />
|-<br />
! Input species !! Allowable symbols/IDs (example)<br />
|-<br />
| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)<br />
|-<br />
| ''R. norvegicus'' || [http://rgd.mcw.edu RGD] gene symbol (e.g. Cdk1) or gene ID (e.g. 2319); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 54237)<br />
|-<br />
| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)<br />
|-<br />
| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)<br />
|-<br />
| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)<br />
|-<br />
| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)<br />
|-<br />
| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)<br />
|-<br />
| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)<br />
|-<br />
| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)<br />
|-<br />
|}<br />
<br />
Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.<br />
<br />
<br />
On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.<br />
For DIOPT-based searches, the columns are:<br />
* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database<br />
* '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''Score''': the number of tools that support a given orthologous gene-pair relationship compared to the total number of tools that compute orthology relationships for those two species (expressed as "X of Y")<br />
* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species<br />
* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)<br />
* '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site<br />
* '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila<br />
The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.<br />
<br />
In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.<br />
<br />
Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. For DIOPT-based searches, it has the following columns:<br />
* '''query_context''': the entered search term<br />
* '''query_species''': the selected input species<br />
* '''query_gene''': the matched input gene symbol<br />
* '''target_species''': the selected output species<br />
* '''ortholog_gene''': official gene symbol, as used in the relevant model organism database<br />
* '''ortholog_gene_reports''': gene IDs at model organism databases, NCBI, Ensembl and/or OMIM<br />
* '''source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship<br />
* '''score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship<br />
* '''best_score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene<br />
* '''best_reverse_score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search<br />
* '''transgene_in_fly''': Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila<br />
The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.<br />
<br />
For DIOPT-based searches, clicking on the '''Exclude scores <3''' text at the top of the results page will remove any ortholog calls with a DIOPT score less than 3 (i.e. only 1 or 2 individual prediction tools support that particular call), which is useful if the unfiltered list is long owing to many low scoring calls. The text switches to '''Show scores <3''', and clicking again reverts back to the full list.<br />
<br />
===Phenotype tab===<br />
<br />
This tool allows searching for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination.<br />
<br />
The top section searches for alleles with a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class] (e.g. "lethal" or "behavior defective"). You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage] (e.g. an embryonic stage) and/or under particular conditions (e.g. "recessive" or "heat sensitive").<br />
<br />
The bottom section searches for alleles that show a phenotype in a particular tissue or cell type (e.g. "wing" or "RP2 neuron"). This uses terms from the [http://{{flybaseorg}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary]. Again, you can refine this search further using the refinement boxes.<br />
<br />
A coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype. The refinement boxes will only suggest terms that have been curated in combination with the main search term. Please note that this auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.<br />
<br />
Please see the related Video Tutorial [https://www.youtube.com/watch?v=hZgsDPypZvk 'Finding genes with similar phenotypes'].<br />
<br />
===Protein Domains tab===<br />
<br />
Search for genes whose product(s) have a specified domain, repeat or site, or belong to a particular protein family, as defined by [https://www.ebi.ac.uk/interpro/ InterPro]. (See the InterPro [http://www.ebi.ac.uk/interpro/faqs.html FAQs] page for an explanation of different signature types.)<br />
<br />
To use, either start typing and select an InterPro term from the [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] suggestions (recommended) or enter your own term, using [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) if desired. Next, choose whether to search ''D. melanogaster'' genes '''only''', or check the box to include other Drosophila species. Then click the 'Search' button or press 'enter'. Resulting hits will be genes whose protein products are associated with an InterPro signature that wholly or partially matches your search term. E.g. A search for 'Ubiquitin' will retrieve hits to the InterPro family 'Ubiquitin', as well as other InterPro signatures that contain that word ('Ubiquitin domain', 'Ubiquitin conserved site' etc.). If you wish to retrieve hits annotated with a specific InterPro signature, then the InterPro ID (e.g. 'IPR019956') should be used.<br />
<br />
===References tab===<br />
<br />
This tab searches the extensive FlyBase bibliography. To use, first select which fields you wish to search by checking the appropriate box(es) at the top, then enter one or more search term(s) as appropriate. Note that certain fields allow the use of Boolean operators (AND, OR, NOT), the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..), and the FlyBase [http://flybase.org/wiki/FlyBase:QuickSearch#Auto-completion auto-complete] feature is active in applicable fields. [http://flybase.org/wiki/FlyBase:QuickSearch#Wild_Cards wildcard(s)] (*) can be added to any search term except for 'Year'.<br />
This functionality is summarized in the following table:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Field !! Boolean terms accepted? !! Auto-complete active? !! Wild cards accepted? !! Example<br />
|-<br />
| '''Author''' || Yes || Yes || Yes || Smith NOT Johnson<br />
|-<br />
| '''Year''' || Yes || No || No || 2004-2008<br />
|-<br />
| '''Title/Abstract''' || No || No || Yes || metabolomics<br />
|-<br />
| '''Journal''' || Yes || Yes || Yes || Dev. Biol.<br />
|-<br />
| '''FBrf/PMID/PMCID/DOI''' || No || No || Yes || paper<br />
|-<br />
| '''Publication type''' || Yes || Yes || Yes || FBrf0126983<br />
|-<br />
| '''All report fields''' || No || No || Yes || dpp<br />
|-<br />
|}</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169167FlyBase:Human Disease Model Report2017-12-13T00:05:10Z<p>Sian: /* Sources of Stocks */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169165FlyBase:Human Disease Model Report2017-12-13T00:03:57Z<p>Sian: /* Selected Drosophila classical alleles */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm/ BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://{{flybaseorg}}/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169163FlyBase:Human Disease Model Report2017-12-13T00:01:13Z<p>Sian: /* RNAi constructs available */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm/ BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169162FlyBase:Human Disease Model Report2017-12-12T23:59:47Z<p>Sian: /* Selected Drosophila transgenes */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm/ BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169161FlyBase:Human Disease Model Report2017-12-12T23:57:53Z<p>Sian: /* Selected mammalian transgenes */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm/ BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Recombinant_Construct_Report Recombinant Construct Report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://{{flybaseorg}}/wiki/FlyBase:Stock_Report Stock Report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sianhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Human_Disease_Model_Report&diff=169160FlyBase:Human Disease Model Report2017-12-12T23:54:42Z<p>Sian: /* Alleles Reported to Model Human Disease (Disease Ontology) */</p>
<hr />
<div>Last Updated: 11 Dec. 2017<br />
<br />
This is a field-by-field guide to the information provided in the '''Human Disease Model Report'''.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Name'''|| style="width: 80%;" | The valid full name that is used in FlyBase for the Human Disease Model.<br />
|-<br />
|'''FlyBase ID'''|| The Primary FlyBase identifier number of the human disease, used to uniquely identify the Human Disease Model in the database. <br />
|-<br />
|'''Disease Ontology ID'''|| Links to [http://disease-ontology.org/ Disease Ontology] term report in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|-<br />
|'''Parent Disease '''|| Links to parent entity, which describes general and shared information for the phenotypic series. Specific (child) diseases are usually defined by a single causative human gene.<br />
|-<br />
|'''OMIM'''|| Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Parent Disease DOID '''|| Links to [http://disease-ontology.org/ Disease Ontology] term report for the Parent Disease in the [http://{{flybaseorg}}/static_pages/termlink/termlink.html Vocabularies] tool.<br />
|}<br />
<br />
==Overview==<br />
<br />
The Overview is a brief summary of the ''Drosophila'' human disease model. For specific disease models, it includes (1) the FlyBase disease name, any abbreviation commonly used, and the pattern of inheritance in human (e.g., autosomal dominant); (2) the human gene implicated, with a brief mention of known or postulated function and whether it is implicated in any additional diseases; (3) the Drosophila ortholog(s) of the implicated human gene, the nature of available genetic reagents for that gene, and whether other human genes are orthologous to that fly gene; (4) whether the human gene has been transgenically introduced into flies, the nature of transgenically expressed constructs, whether the human gene has been used to heterologously rescue Drosophila loss-of-function phenotypes; (5) variants implicated in human disease that have been characterized, whether in the context of a transgenic human gene or an analagous mutation in the fly gene; (6) highlights of phenotype(s) of the fly gene and whether genetic and/or physical interaction data are available. Records that do not conform to this pattern include reports for phenotypic series and for induced models (diet- or chemically-induced, for example). The Overview is date-stamped to reflect the last curator update.<br />
<br />
==Disease Summary Information==<br />
<br />
===Parent Disease Summary===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symptoms and phenotype '''|| style="width: 80%;" | Describes symptoms and phenotypes shared by diseases in the relevant phenotypic series. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|}<br />
<br />
===Specific Disease Summary===<br />
<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM report '''|| style="width: 80%;" | Links to relevant [http://omim.org/ OMIM] phenotype report.<br />
|-<br />
|'''Symptoms and phenotype '''|| Describes symptoms and phenotypes characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Genetics '''|| Describes the genetics of the disease, including causative human gene, and pattern of inheritance. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Cellular phenotype and pathology '''|| Describes the cellular phenotype and pathology characteristic of the disease. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''Molecular information '''|| Describes molecular information relevant to the disease, including information about the function of the causative gene, molecular information about mutations in the causative gene, and/or molecular information about mutant isoforms of the causative protein. Entry includes links to outside source, and is date-stamped as to when a FlyBase curator last consulted the source.<br />
|-<br />
|'''External links '''|| A list of links to external databases and resources providing additional background concerning the disease. These include:<br />
<br />
[http://www.genecards.org/ Gene Cards]<br />
<br />
[http://www.ncbi.nlm.nih.gov/books/ GeneReviews, NCBI Bookshelf]<br />
<br />
[http://ghr.nlm.nih.gov/condition/ Genetics Home Reference (condition)]<br />
<br />
[http://ghr.nlm.nih.gov/gene/ Genetics Home Reference (gene)]<br />
<br />
[http://ghr.nlm.nih.gov/geneFamily/ Genetics Home Reference (geneFamily)]<br />
<br />
[http://www.kegg.jp/kegg/pathway.html/ KEGG Disease Pathways]<br />
<br />
[https://www.ncbi.nlm.nih.gov/medgen/ NCBI MedGen]<br />
<br />
[https://www.ncbi.nlm.nih.gov/gene/ NCBI (Entrez) gene]<br />
<br />
[http://www.gene2function.org/search/get_ortholog/9606/ Gene2Function (human gene)]<br />
<br />
[http://marrvel.org/search/gene/ MARRVEL (gene)]<br />
<br />
[http://www.informatics.jax.org/disease/ MGI Human-Mouse Disease Connection]<br />
|-<br />
|'''Disease synonyms '''|| A listing of other names, abbreviations, acronyms and terms that have been used to refer to the disease.<br />
|}<br />
<br />
==Related Diseases==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Related human health report(s) '''|| style="width: 80%;" | Links to the Report(s) of disease(s) that are related to the disease that is the subject of a Human Disease Model Report, but is not a member of the same phenotypic series. For example, the diseases could be related by having the same causative human gene.<br />
|}<br />
<br />
===Related Specific Diseases===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''OMIM phenotypic series '''|| style="width: 80%;" | Links to relevant [https://omim.org/phenotypicSeriesTitle/all OMIM phenotypic series]. An OMIM phenotypic series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.<br />
|}<br />
<br />
A table that consists of four columns:<br />
<br />
'''Disease''' - Consists of OMIM symbol, links to OMIM phenotype report.<br />
<br />
'''Associated Human gene(s)''' - Consists of OMIM symbol, links to OMIM genotype report.<br />
<br />
'''Drosophila model''' - Consists of valid full name that is used in FlyBase for the disease, links to Human Disease Model Report.<br />
<br />
'''Human transgene in Drosophila''' - "y" or no entry; has the human ortholog been transgenically expressed in flies.<br />
<br />
==Ortholog Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Human gene (HGNC) '''|| style="width: 80%;" | Links to HUGO Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]) symbol report.<br />
|-<br />
|'''Human gene (FlyBase) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of human gene transgenically expressed in flies.<br />
|-<br />
|'''D. melanogaster ortholog (based on DIOPT) '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of ''Drosophila'' gene orthologous to HGNC gene. Orthology determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis resulting from the combined predictions of 10 ortholog prediction algorithms.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the human to ''Drosophila'' gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction.<br />
|-<br />
|'''Other mammalian ortholog(s) used '''|| Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of nonhuman mammalian gene transgenically expressed in flies.<br />
|}<br />
<br />
==D. melanogaster Gene Information==<br />
Drosophila gene(s) identified as model(s) of this disease.<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Molecular function (GO)'''|| style="width: 80%;" | A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Cellular component (GO)'''|| A summary of the [http://geneontology.org/ Gene Ontology] [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the ''Drosophila'' gene orthologous to the causative human gene.<br />
|-<br />
|'''Comments on ortholog(s) '''|| Comments on the nature of the orthology of the ''Drosophila'' to human gene(s), e.g., one to one, one to many, many to one, many to many, as defined by [http://orthodb.org/ OrthoDB] ortholog prediction. Comment concerning protein identity and similarity between Drosophila protein and the human ortholog; alignment determined by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] analysis<br />
|-<br />
|'''Orthologs and Alignments from DRSC '''|| Links to [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl/ DIOPT] tool; the H.sapiens (Human) link pre-fills the DIOPT interface with the ''Drosophila'' gene to search for its human ortholog.<br />
|}<br />
<br />
==Synthetic Gene(s) Used==<br />
<br />
Links to FlyBase [http://{{flybaseorg}}/wiki/FlyBase:Gene_Report Gene Report] of artificial gene transgenically expressed in flies (e.g. a CAG repeat construct or hexanucleotide repeat construct). Such genes have the feature type engineered_foreign_region.<br />
<br />
==Experimental Findings==<br />
<br />
===Summary===<br />
<br />
This section used only for original test-case disease model reports; for most human disease model reports this section is blank.<br />
<br />
===Description of Experiments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Mammalian transgenics: heterologous rescue ''' || style="width: 80%;" | Free text description of use of human or other mammalian transgene to rescue loss-of-function phenotypes of a mutation in its orthologous ''Drosophila'' gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: transgenic phenotype '''|| Free text description of phenotypes resulting from tissue-specific transgenic expression of human or other mammalian disease-associated protein, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Mammalian transgenics: interactions '''|| Free text description of genetic and/or physical interactions observed between transgenically expressed human or other mammalian protein and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|-<br />
|'''Mammalian transgenics: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from transgenically expressed human or other mammalian protein, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: relevant phenotypes '''|| Free text description of phenotypes resulting from mutations in or RNAi knockdown of the ''Drosophila'' ortholog of a human disease-associated gene, with a focus on disease model relevance. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: interactions '''|| Free text description of genetic and/or physical interactions observed between the ''Drosophila'' ortholog of a human disease-associated gene and Drosophila genes/proteins and/or other transgenically expressed human or mammalian genes/proteins, with a focus on disease model relevance .A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila genes: pertubations and treatments '''|| Free text description of the effect of chemical or environmental perturbations or treatments on the phenotypes resulting from mutations in, RNAi knockdown of, or transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene,, with a focus on disease model relevance. This field is also used to describe drug discovery and/or drug screening experiments. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Drosophila recombinant constructs: phenotype or rescue '''|| Free text description of phenotypes resulting from transgenic overexpression of the ''Drosophila'' ortholog of a human disease-associated gene, or of the use of ''Drosophila'' transgene to rescue loss-of-function phenotypes of a mutation in the ''Drosophila'' ortholog of a human disease-associated gene. A listing of genetic reagents used in experiments, linked to relevant [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports], are appended to the end of the statement. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Additional information '''|| Free text descriptions of experiments that are not covered in other descriptive fields, including but not exclusive to gene expression patterns, experiments conducted in cell culture, details of protein structural domains or gene models, and experiments or observations in other organisms. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|-<br />
|'''Proposed mechanisms '''|| Free text description of key findings concerning disease mechanism that have been discovered or confirmed in ''Drosophila'' experiments. Every statement is linked to a supporting [http://{{flybaseorg}}/wiki/FlyBase:Reference_Report Reference Report].<br />
|}<br />
<br />
==Summary of Physical Interactions==<br />
<br />
Information regarding curated physical interactions for the protein and RNA products of the gene. Currently, only interactions involving two D. melanogaster genes are reported. Only pair-wise interactions are reported. Information is imported from existing [http://{{flybaseorg}}/wiki/FlyBase:Interaction_Report Interaction Reports].<br />
<br />
==Alleles Reported to Model Human Disease (Disease Ontology)==<br />
<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - If the allele models the phenotype on its own 'Inferred from mutant phenotype' is displayed. If the mutant phenotype is only observed in combination with another allele 'In combination with' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|-<br />
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of four columns<br />
<br />
'''Allele''' - The alleles of the gene that is being used as a model.<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
<br />
This information is also shown on the individual [http://{{flybaseorg}}/wiki/FlyBase:Allele_Report Allele Reports].<br />
|}<br />
<br />
==Genetic Tools, Stocks and Reagents==<br />
<br />
===Sources of Stocks===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Bloomington Stock Center Disease Page'''|| style="width: 80%;" | Links to relevant [http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm/ BDSC Human Disease Model page].<br />
|}<br />
<br />
===Selected mammalian transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the human or other mammalian transgene.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the human or other mammalian transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those human or mammalian transgenes available from a public stock center.<br />
<br />
===Selected Drosophila transgenes===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' transgene.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the ''Drosophila'' transgene.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' transgenes available from a public stock center.<br />
<br />
===RNAi constructs available===<br />
<br />
A table that consists of three columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the RNAi construct.<br />
<br />
'''Transgene''' - Links to the [http://flybase.org/wiki/FlyBase:Recombinant_Construct_Report/ recombinant construct report] for the RNAi construct.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those RNAi constructs available from a public stock center.<br />
<br />
===Selected Drosophila classical alleles===<br />
<br />
A table that consists of four columns:<br />
<br />
'''Allele''' - Links to the [http://flybase.org/wiki/FlyBase:Allele_Report/ allele report] for the ''Drosophila'' classical mutant.<br />
<br />
'''Allele class''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the allele class to which the allele belongs.<br />
<br />
'''Mutagen''' - Lists the [http://flybase.org/wiki/FlyBase:Controlled_vocabularies_used_by_FlyBase/ FlyBase CV term] for the mutagen responsible for the genetic lesion causing the mutation.<br />
<br />
'''Publicly Available Stocks''' - Links to the [http://flybase.org/wiki/FlyBase:Stock_Report/ stock report] for those ''Drosophila'' classical mutants available from a public stock center.<br />
<br />
===References===<br />
<br />
A list of publications that discuss the human disease model, subdivided into fields by type of publication.</div>Sian