Difference between revisions of "FlyBase:Gene Report"

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Last Updated: 16 September 2015
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Last Updated: 14th October 2022
  
  
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As well as including gene reports for genes derived from species within the family Drosophilidae, FlyBase also includes 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.
 
As well as including gene reports for genes derived from species within the family Drosophilidae, FlyBase also includes 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.
  
−
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data.  
+
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data.  
  
 
This is a field-by-field guide to the information provided in the Gene Report.
 
This is a field-by-field guide to the information provided in the Gene Report.
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|'''Stock availability'''    || A list of experimental lines relating to this gene that are available for order from public stock centers.
 
|'''Stock availability'''    || A list of experimental lines relating to this gene that are available for order from public stock centers.
 
|-
 
|-
−
|'''Gene Snapshot'''    || A short summary designed to provide a quick overview of the function of the gene's products.
+
|'''Enzyme Name (EC)'''    || Where relevant, the systematic name(s) for an enzyme together with its Enzyme Commission (EC) number(s). These data are derived from our Gene Ontology (GO) Molecular Function annotations by using the EC cross-references within the GO. Each EC number is linked to the corresponding page at the [https://enzyme.expasy.org ExPASy ENZYME database].
−
It is based on key points solicited from expert researchers, and revised by FlyBase curators. The review date is stated, and cases that are in progress or are deemed to have insufficient data to summarize are stated as such.
 
 
|-
 
|-
−
|'''Other Summaries'''    || Links to the summaries available for this gene.
+
|'''Gene Summary'''    || A summary is shown at the top of every D. melanogaster gene report, with precedence given to the manually written Gene Snapshot. Where a Gene Snapshot is unavailable, a summary contributed by UniProtKB, Interactive Fly, Alliance of Genome Resources or the automated FlyBase gene summary is shown instead.
 +
|-
 +
|'''All Summaries'''    || Links to all the summaries available for this gene.
 
|-
 
|-
 
|'''Also Known As'''    || Symbol synonyms that do not match the current gene symbol or annotation ID but have been used to refer to the gene in at least two papers. A maximum of ten case-insensitive synonyms are shown - when synonyms differ only by case, the version associated with most papers is reported.
 
|'''Also Known As'''    || Symbol synonyms that do not match the current gene symbol or annotation ID but have been used to refer to the gene in at least two papers. A maximum of ten case-insensitive synonyms are shown - when synonyms differ only by case, the version associated with most papers is reported.
 
|-
 
|-
−
|'''Comparative Info'''    || Link to corresponding gene page at the [http://www.alliancegenome.org/ Alliance of Genome Resources] website.
+
|'''Keys Links'''    || Links to the corresponding pages at other key bioinformatic resources, specifically the [http://www.alliancegenome.org/ Alliance of Genome Resources], [https://www.ncbi.nlm.nih.gov/gene NCBI Gene], [http://www.ensembl.org/index.html Ensembl], [https://www.uniprot.org UniProtKB] (canonical isoform from the gene-centric reference proteome (GCRP)) and [https://rnacentral.org RNAcentral], the latter two dependent on whether the gene is protein-coding or not. Full and explicit crossreferences for these and other resources are shown in the ‘External Crossreferences and Linkouts’ section.
 
|}
 
|}
  
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This field is only filled in for genes with annotations.
 
This field is only filled in for genes with annotations.
 
|-
 
|-
−
|'''Genomic Maps'''    || A [http://{{flybaseorg}}/cgi-bin/gbrowse2/dmel/ GBrowse] thumbnail showing the location of the gene (highlighted in yellow) in the genome. Clicking on any of the genes visible in the thumbnail will take you to the corresponding gene report.
+
|'''Recombination Map'''    || A computed genetic map position for the gene.
−
 
+
|-
−
 
+
|'''RefSeq locus'''    || The RefSeq locus ID for the chromosomal scaffold containing the gene, and the coordinates of the gene within that scaffold. Linked to the corresponding RefSeq entry.
−
To the left of the GBrowse thumbnail, there are links to the [http://{{flybaseorg}}/cgi-bin/gbrowse2/dmel/ GBrowse] and [http://{{flybaseorg}}/jbrowse/?data=data/json/dmel JBrowse] tool.
+
|-
−
 
+
|'''Sequence'''    || There are options for downloading sequences associated with the gene. The drop-down menu allows the selection of the sequence of interest. The button beneath returns the sequence via the [http://{{flybaseorg}}/download/sequence Sequence Downloader] tool.
−
 
 
−
To the right of the GBrowse thumbnail, there are options for downloading sequences associated with the gene. The drop-down menu allows the selection of the sequence of interest. The button beneath returns the sequence via the [http://{{flybaseorg}}/download/sequence Sequence Downloader] tool.
 
−
 
 
 
The following sequences can be downloaded:
 
The following sequences can be downloaded:
  
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3' UTR
 
3' UTR
 +
|-
 +
|'''Genomic Maps'''    || A [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2R%3A13437076..13452701&tracks=Gene_span%2CGene&highlight= JBrowse] thumbnail showing the location of the gene (highlighted in yellow) in the genome. Clicking on any of the genes visible in the thumbnail will take you to the corresponding gene report.
 +
 +
 +
To the left of the JBrowse thumbnail, there are links to the  [http://{{flybaseorg}}/jbrowse/?data=data/json/dmel JBrowse] tool.
 
|-
 
|-
 
|'''Other Genome Views'''    || Links to external genome browsers.
 
|'''Other Genome Views'''    || Links to external genome browsers.
 
|}
 
|}
  
−
==Tag or Foreign Gene Data==
+
==Foreign Gene Data==
 +
 
 +
This section is only displayed in an individual Gene Report is for a "foreign gene", i.e. any non-drosophilid gene that has been introduced into Drosophila, for example via a transgenic construct. This section shows the species from which the gene is derived, the gene symbol, and where possible an accession number for the gene (either an identifier number from a human or model organism database, or a sequence accession number).
 +
 
 +
==Function==
 +
 
 +
{| class="wikitable" style="width: 100%;"
 +
|-
 +
|'''GO Summary Ribbons'''    || style="width: 80%;" | '''GO Summary Ribbons''' are graphical summaries, designed to give an immediate overview of a gene product's properties and depth of characterization. They are derived from the [http://geneontology.org/ Gene Ontology (GO)]  terms associated with the gene, divided into aspects of molecular function, biological process and cellular component. The GO annotations are grouped under high-level summary categories and are presented as colored cells in the row or 'ribbon' (see mapping table below for details). The depth of color of each cell indicates how many unique terms are grouped in a particular category. The unique terms that group under a particular cell can be seen by mousing-over the cell. Some terms may group under more than one cell because the GO allows multiple ancestry.
 +
|-
 +
|'''Gene Ontology (GO) Annotations'''    || style="width: 80%;" | [http://geneontology.org/ Gene Ontology] (GO) [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] (CV) terms assigned to genes based on evidence in external publications and internal analysis. Note that terms are assigned to genes but apply to the product of that gene. The number in parentheses shows the total number of different terms assigned to a gene. 
  
−
This section is only displayed in an individual Gene Report if the gene is a "tag" or a "foreign gene". (A "tag" is a DNA fragment that is used to confer a novel property to a gene product, and may be artificial or derived from a Drosophilid or non-drosophilid gene. A "foreign gene" is any non-drosophilid gene that has been introduced into Drosophila, for example via a transgenic construct.) For tags, this section shows the species from which the gene is derived, the nature of the tag, and either a sequence accession number (if available) or a brief description of the tag. For foreign genes, this section shows the species from which the gene is derived, the gene symbol, and where possible an accession number for the gene (either an identifier number from a human or model organism database, or a sequence accession number).
+
Annotations are divided into three subsections:
  
−
==GO summary ribbons==
+
[https://geneontology.github.io/docs/ontology-documentation/ '''Molecular Function''']
  
−
'''GO Summary Ribbons''' are graphical summaries, designed to give an immediate overview of a gene product's properties and depth of characterization. They are derived from the [http://geneontology.org/ Gene Ontology (GO)]  terms associated with the gene, divided into aspects of molecular function, biological process and cellular component. The GO annotations are grouped under high-level summary categories and are presented as colored cells in the row or 'ribbon'. The depth of color of each cell indicates how many unique terms are grouped in a particular category. The unique terms that group under a particular cell can be seen by mousing-over the cell. Some terms may group under more than one cell because the GO allows multiple ancestry.
+
[https://geneontology.github.io/docs/ontology-documentation/ '''Biological Process''']
−
In the top left corner, '''Detailed GO annotations''' links to the [[FlyBase:Gene_Report#Gene_Ontology:_Function.2C_Process_.26_Cellular_Component|Gene Ontology]] section of the report, where the annotations are displayed in full.
 
  
−
==Families, Domains and Molecular Function==
+
[https://geneontology.github.io/docs/ontology-documentation/ '''Cellular Component''']
 +
 
 +
Within each subsection the terms are divided into ''''Terms Based on Experimental Evidence'''' and ''''Terms Based on Predictions or Assertions''''.
 +
 
 +
'''GO term''': Clicking on the term in the '''CV term''' column will take you to the relevant GO [[FlyBase:Controlled vocabularies used by FlyBase|CV Term Report]], which includes a definition of the GO term.
 +
 
 +
'''Gene product to term relations''': GO CV terms are preceded by a [[FlyBase:Gene_Ontology_(GO)_Annotation#G.3.2.2._Use_of_Gene_Product_To_Term_Relations|gene product to term relation]] which imparts a relational meaning between the term and the gene product.
 +
 
 +
'''NOT''': The qualifier [[FlyBase:Gene_Ontology_(GO)_Annotation#G.3.2.3. Use of negation|NOT]] is used to make an explicit note that the gene product is not associated with the GO term.
 +
 
 +
'''Evidence''': The type of evidence used to support the GO term is indicated in the evidence column. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology [http://geneontology.org/page/guide-go-evidence-codes Guide to GO Evidence Codes]. Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the [http://www.geneontology.org/doc/GO.xrf_abbs GO.xrf_abbs] file. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
 +
 
 +
More information about how GO terms are assigned can be found under the [[FlyBase:Gene Ontology (GO) Annotation#Classification of Gene Products using Gene Ontology (GO) terms|Classification of Gene Products using Gene Ontology (GO) terms]].  The current release of GO data for all FlyBase genes can be found in the [http://{{flybaseorg}}/static_pages/downloads/current/go/gene_association.fb.gz gene_association.fb file]. The latest version of this data is available for download [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.fb.gz here] from the Gene Ontology consortium site. Details about the file format and comments on version differences can be found in the documentation on the [[FlyBase:Gene Ontology (GO) Annotation#Classification of Gene Products using Gene Ontology (GO) terms|Classification of Gene Products using Gene Ontology (GO) terms]]
 +
|-
 +
|'''Gene Group (FlyBase)'''    || style="width: 80%;" | Lists any FlyBase Gene Groups the gene is a member of, with a link to the [[FlyBase:Gene Group Report|Gene Group Report]].
 +
|-
 +
|'''Pathway (FlyBase)'''    || style="width: 80%;" | Lists any FlyBase Pathways the gene is a member of, with a link to the [[FlyBase:Pathway_Report|Pathway Report]].
 +
|-
 +
|'''Protein Family (UniProt)'''    || Lists any [http://www.uniprot.org/ UniProt] Protein Families shown in their 'Sequence similarities' section, with the evidence code and a link to corresponding UniProt page.
 +
|-
 +
|'''Protein Signatures (InterPro)'''    ||  Lists [http://www.ebi.ac.uk/interpro/ InterPro] protein domains or motifs found in the protein encoded by the gene with link to the corresponding InterPro page.
 +
|-
 +
|'''Catalytic Activity (EC/Rhea)''' || Where relevant, the reaction(s) catalyzed by an enzyme together with their Enzyme Commission (EC) number(s) and RHEA ID(s). These data are derived from our Gene Ontology (GO) Molecular Function annotations by using the EC/Rhea cross-references within the GO. EC numbers are linked to the corresponding page at the [https://enzyme.expasy.org ExPASy ENZYME database], and RHEA IDs are linked to the corresponding page at the [https://www.rhea-db.org Rhea database]. Clicking on an image of reactant/product in the Rhea graphic links to the corresponding page at the [https://www.ebi.ac.uk/chebi/init.do ChEBI] database.
 +
|}
 +
 
 +
 
 +
'''GO Summary Ribbon mapping tables:'''
 +
 
 +
 
 +
'''molecular function'''
 +
 
 +
slimming path relations: is_a, part_of
  
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Gene Group Membership (FlyBase)'''    || style="width: 80%;" | Lists any Flybase Gene Groups the gene is a member of, with a link to the [[FlyBase:Gene Group Report|Gene Group Report]].
+
! Tile Name
 +
! GO term(s)
 +
! GO ID(s)
 +
|-
 +
| enzyme
 +
| catalytic activity
 +
| GO:0003824
 +
|-
 +
| regulator
 +
| molecular function regulator
 +
| GO:0098772
 +
|-
 +
| receptor
 +
| signaling receptor activity
 +
| GO:0038023
 +
|-
 +
| receptor binding
 +
| signaling receptor binding
 +
| GO:0005102
 +
|-
 +
| transporter
 +
| transporter activity
 +
| GO:0005215
 +
|-
 +
| structural molecule
 +
| structural molecule activity
 +
| GO:0005198
 +
|-
 +
| cytoskeleton binding
 +
| cytoskeletal protein binding
 +
| GO:0008092
 +
|-
 +
| DNA binding
 +
| DNA binding
 +
| GO:0003677
 +
|-
 +
| RNA binding
 +
| RNA binding
 +
| GO:0003723
 +
|-
 +
| transcription factor
 +
| transcription regulator activity
 +
| GO:0140110
 +
|-
 +
| small molecule binding
 +
| small molecule binding
 +
| GO:0036094
 +
|-
 +
| metal ion binding
 +
| metal ion binding
 +
| GO:0046872
 
|-
 
|-
−
|'''Protein Family (UniProt, Sequence Similarities)'''    || Lists any UniProt Protein Families shown in their 'Sequence similarities' section, with the evidence code and a link to corresponding [http://www.uniprot.org/ UniProt] page.
+
| lipid binding
 +
| lipid binding
 +
| GO:0008289
 
|-
 
|-
−
|'''Protein Domains/Motifs'''    || '''Interpro'''  Lists Protein Domains or motifs found in the protein encoded by the gene with link to the corresponding [http://www.ebi.ac.uk/interpro/ Interpro] page.
+
| carbohydrate binding
 +
| carbohydrate binding
 +
| GO:0030246
 
|-
 
|-
−
|'''Molecular Function (see GO section for details)''' || A summary of the [http://geneontology.org/ Gene Ontology] Molecular Function terms associated with the gene, divided into terms with '''Experimental Evidence''' and '''Predictions/Assertions'''. Each term is linked to the appropriate '''Term Report'''.
+
| other molecular_function
 +
| Any term that does not map to the above
 +
| Any ID that does not map to the above
 +
|}
  
−
For the full [http://geneontology.org/ Gene Ontology] (GO) data, including evidence and attributions, see the [[FlyBase:Gene_Report#Gene_Ontology:_Function.2C_Process_.26_Cellular_Component|Gene Ontology]] section.
+
 
 +
'''biological process'''
 +
 
 +
slimming path relations: is_a, part_of, regulates
 +
 
 +
 
 +
{| class="wikitable" style="width: 100%;"
 +
|-
 +
! Tile Name
 +
! GO term(s)
 +
! GO ID(s)
 +
|-
 +
| cell cycle/proliferation
 +
| cell cycle,cell proliferation
 +
| GO:0008283, GO:0007049
 +
|-
 +
| cellular organization/biogenesis
 +
| cellular component organization or biogenesis
 +
| GO:0071840
 +
|-
 +
| cellular transport/localization
 +
| macromolecule localization, establishment of localization
 +
| GO:0051234, GO:0033036
 +
|-
 +
| development
 +
| developmental process
 +
| GO:0032502
 +
|-
 +
| reproduction
 +
| reproduction
 +
| GO:0000003
 +
|-
 +
| immune system
 +
| immune system process
 +
| GO:0002376
 +
|-
 +
| nervous system process
 +
| nervous system process
 +
| GO:0050877
 +
|-
 +
| behavior
 +
| behavior
 +
| GO:0007610
 +
|-
 +
| response to stimulus
 +
| response to stimulus
 +
| GO:0050896
 +
|-
 +
| signaling
 +
| signaling
 +
| GO:0023052
 +
|-
 +
| gene expression
 +
| gene expression
 +
| GO:0010467
 +
|-
 +
| protein metabolism
 +
| protein metabolic process
 +
| GO:0019538
 +
|-
 +
| DNA metabolism
 +
| DNA metabolic process
 +
| GO:0006259
 +
|-
 +
| small molecule metabolism
 +
| small molecule metabolic process
 +
| GO:0044281
 +
|-
 +
| other biological_process
 +
| Any term that does not map to the above
 +
| Any ID that does not map to the above
 
|}
 
|}
 +
 +
 +
'''cellular component'''
 +
 +
slimming path relations: is_a, part_of
 +
 +
{| class="wikitable" style="width: 100%;"
 +
|-
 +
! Tile Name
 +
! GO term(s)
 +
! GO ID(s)
 +
|-
 +
| extracellular
 +
| extracellular region
 +
| GO:0005576
 +
|-
 +
| cytosol
 +
| cytosol
 +
| GO:0005829
 +
|-
 +
| cytoskeleton
 +
| cytoskeleton
 +
| GO:0005856
 +
|-
 +
| mitochondrion
 +
| mitochondrion
 +
| GO:0005739
 +
|-
 +
| nucleus
 +
| nucleus
 +
| GO:0005634
 +
|-
 +
| chromosome
 +
| chromosome
 +
| GO:0005694
 +
|-
 +
| membrane
 +
| membrane
 +
| GO:0016020
 +
|-
 +
| cell periphery
 +
| cell periphery
 +
| GO:0071944
 +
|-
 +
| cell projection
 +
| cell projection
 +
| GO:0042995
 +
|-
 +
| endomembrane system
 +
| vacuole, endomembrane system
 +
| GO:0005773, GO:0012505
 +
|-
 +
| synapse
 +
| synapse
 +
| GO:0045202
 +
|-
 +
| macromolecular complex
 +
| protein-containing complex
 +
| GO:0032991
 +
|-
 +
| other cellular_component
 +
| Any term that does not map to the above
 +
| Any ID that does not map to the above
 +
|}
 +
 
==Summaries==
 
==Summaries==
  
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
  
−
|'''Gene Snapshot'''    || style="width: 80%;" | A short summary designed to provide a quick overview of the function of the gene's products.
+
|'''Gene Snapshot'''    || style="width: 80%;" | A short summary designed to provide a quick overview of the function of the gene's products. It is based on key points solicited from expert researchers, and revised by FlyBase curators. The review date is stated, and cases that are in progress or are deemed to have insufficient data to summarize are stated as such.
−
It is based on key points solicited from expert researchers, and revised by FlyBase curators. The review date is stated, and cases that are in progress or are deemed to have insufficient data to summarize are stated as such.
+
|-
 +
|'''Automated Description (Alliance of Genome Resources)'''    || style="width: 80%;" | Automated, standardised descriptions for D. melanogaster and human genes imported from [https://www.alliancegenome.org The Alliance of Genome Resources].  These descriptions currently summarize data on gene function, disease associations and orthology to human genes.  
 
|-
 
|-
−
|'''FlyBase Automatically Generated Summary'''    || style="width: 80%;" | Generated automatically from information in the '''gene report''' and related [[FlyBase:Allele_Report|allele reports]]. For more information about each statement in the summary see the relevant section in the gene gene/allele report.
+
|'''Automatically Generated Summary (FlyBase )'''    || style="width: 80%;" | Generated automatically by FlyBase from information in the '''gene report''' and related [[FlyBase:Allele_Report|allele reports]]. For more information about each statement in the summary see the relevant section in the gene gene/allele report.
 
|-
 
|-
−
|'''Gene Group Membership'''    || style="width: 80%;" | Each FlyBase Gene Group that the gene is a member of is listed with a description of that group. The Gene Group name is hyperlinked to the corresponding [[FlyBase:Gene Group Report|Gene Group Report]].
+
|'''Pathway (FlyBase)'''    || style="width: 80%;" | Manually written summary for the FlyBase Pathway Group(s) of which the gene is a member. The Pathway Group name is hyperlinked to the corresponding [[FlyBase:Gene Group Report|Pathway Group Report]].
 
|-
 
|-
−
|'''UniProt Contributed Function Data'''    || style="width: 80%;" | Shows the summary shown in the [http://www.uniprot.org/ UniProt] ''''Function'''' section, with the evidence code and a hyperlink to corresponding [http://www.uniprot.org/ UniProt] page.
+
|'''Gene Group (FlyBase)'''    || style="width: 80%;" | Manually written summary for the FlyBase Gene Group(s) of which the gene is a member. The Gene Group name is hyperlinked to the corresponding [[FlyBase:Gene Group Report|Gene Group Report]].
 
|-
 
|-
−
|'''Red Book'''    || style="width: 80%;" | Phenotypic descriptions of mutants of this gene from the Red Book (Lindsley and Zimm 1992). Gene/Allele symbols may differ from current usage.
+
|'''Protein Function (UniProtKB)'''    || style="width: 80%;" | Shows the summary shown in the [http://www.uniprot.org/ UniProt] ''''Function'''' section, with a hyperlink to corresponding [http://www.uniprot.org/ UniProt] page.
 
|-
 
|-
−
|'''Interactive Fly'''    || style="width: 80%;" | Shows a summary of the gene from [http://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly].
+
|'''Phenotypic Description (Red Book; Lindsley and Zimm 1992)'''    || style="width: 80%;" | Phenotypic descriptions of mutants of this gene from the Red Book (Lindsley and Zimm 1992). Gene/Allele symbols may differ from current usage.
 +
|-
 +
|'''Summary (Interactive Fly)'''    || style="width: 80%;" | Shows a summary of the gene from [http://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly]. Links to the summary on the FlyBase wiki and to the gene page in [http://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly].
 +
|}
  
−
Links to the summary on the FlyBase wiki and to the gene page in [http://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly].
 
−
|}
 
 
==Gene Model & Products==
 
==Gene Model & Products==
−
The number of transcripts abd unique polyptides annotated for the gene are given.
 
  
−
A GBrowse graphic showing the gene model. The grene's transcripts, CDS and any transgene insertion sites in the region are shown. For a more detailed view showing more features, a link to open GBrowse in a separate window is provided above the graphic.
+
===Number of Transcripts===
 +
The number of transcripts annotated for the gene are given.
 +
 
 +
===Number of Unique polypeptides===
 +
The number of unique polypeptides annotated for the gene are given.
 +
 
 +
===JBrowse Graphic===
 +
 
 +
A JBrowse graphic showing the gene model. The grene's transcripts, CDS and any transgene insertion sites in the region are shown. For a more detailed view showing more features, a link to open JBrowse in a separate window is provided above the graphic.
  
 
===Protein Domains (via Pfam)===
 
===Protein Domains (via Pfam)===
Line 166: Line 410:
 
The corresponding [https://www.ebi.ac.uk/interpro InterPro] data is shown in a table below.
 
The corresponding [https://www.ebi.ac.uk/interpro InterPro] data is shown in a table below.
  
−
===Comments on the Gene Model===
+
===Structure===
 +
As appropriate, this section shows a prediction of the 3D protein structure or a 2D RNA structure, where available.
 +
 
 +
====Protein 3D structure (Predicted by AlphaFold)====
 +
For protein-coding genes, this section displays the 3D protein structure predicted by [https://alphafold.ebi.ac.uk AlphaFold]. Only the UniProt 'canonical isoform' is shown for a given protein, and structures are not available for all proteins - see the AlphaFold [https://alphafold.ebi.ac.uk/faq FAQ] for more details. The UniProt accession of the protein is given in the section header and links to the corresponding AlphaFold webpage. The image can be zoomed and rotated using a mouse/trackpad. Several display aspects can be changed and customised using the buttons within the image.
 +
 
 +
====RNA 2D structure (Predicted by RNAcentral)====
 +
For relevant non-coding RNA (ncRNA) genes, this section displays the 2D structure for ncRNAs predicted by [https://www.nature.com/articles/s41467-021-23555-5 R2DT] and as shown within [https://rnacentral.org RNAcentral]. Structured ncRNAs include tRNAs, rRNAs, snRNAs, snoRNAs and the RNA components of RNase P, RNase MRP and SRP. The RNAcentral identifier is given in the section header and links to the corresponding RNAcentral webpage. The image can be zoomed and repositioned using a mouse/trackpad. Several display aspects can be changed and customised using the buttons within and above the image - see the RNAcentral [https://rnacentral.org/help/secondary-structure documentation] for more details.
 +
 
 +
===Comments on Gene Model===
  
 
Comments regarding the annotation of the gene, including whether the gene model contains any unconventional features.
 
Comments regarding the annotation of the gene, including whether the gene model contains any unconventional features.
Line 204: Line 457:
 
Rfam - RNA families database of alignments and CMs
 
Rfam - RNA families database of alignments and CMs
  
−
These links are also displayed together with all other external data links for the gene in the '''EXTERNAL CROSSREFERENCES & LINKOUTS''' section of the Gene Report.
+
These links are also displayed together with all other external data links for the gene in the [[FlyBase:Gene_Report#External Crossreferences & Linkouts| External Crossreferences and Linkouts]] section of the Gene Report.
−
 
 
  
 
===Polypeptide Data===
 
===Polypeptide Data===
Line 224: Line 476:
 
====External Data====
 
====External Data====
  
−
A list of links to external databases that are relevant to the polypeptides encoded by the gene.  
+
A list of links to external databases that are relevant to the polypeptides encoded by the gene. These links are also displayed together with all other external data links for the gene in the [[FlyBase:Gene_Report#External Crossreferences & Linkouts| External Crossrefences and Linkouts]] section of the Gene Report.
−
 
 
−
These links are also displayed together with all other external data links for the gene in the '''EXTERNAL CROSSREFERENCES & LINKOUTS''' section of the Gene Report.
 
  
 
===Sequences Consistent with the Gene Model===
 
===Sequences Consistent with the Gene Model===
Line 244: Line 494:
 
These accessions are both FlyBase curated links and associations made by automated assessment of aligned cDNA and EST nucleotide sequences.
 
These accessions are both FlyBase curated links and associations made by automated assessment of aligned cDNA and EST nucleotide sequences.
  
−
===Mapped Features & Mutations===
+
===Mapped Features===
  
 
A table listing features associated with the gene, additional to the basic transcript and polypeptide structure, that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains the feature's name as well as its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.
 
A table listing features associated with the gene, additional to the basic transcript and polypeptide structure, that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains the feature's name as well as its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.
Line 252: Line 502:
 
A list of links to external databases that are relevant to the gene model as a whole, but not specifically to individual gene products.
 
A list of links to external databases that are relevant to the gene model as a whole, but not specifically to individual gene products.
  
−
These links are also displayed together with all other external data links for the gene in the '''EXTERNAL CROSSREFERENCES & LINKOUTS''' section of the Gene Report.
+
These links are also displayed together with all other external data links for the gene in the [[FlyBase:Gene_Report#External Crossreferences & Linkouts| External Crossreferences and Linkouts]] section of the Gene Report.
  
−
==Gene Ontology: Function, Process & Cellular Component==
+
==Expression Data==
  
−
[http://geneontology.org/ Gene Ontology] (GO) [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] (CV) terms assigned to genes based on evidence in external publications and internal analysis. Note that terms are assigned to genes but apply to the product of that gene. The number in parentheses shows the total number of different terms assigned to a gene.
 
  
−
More information about how GO terms are assigned can be found under the [[FlyBase:Gene Ontology (GO) Annotation#Classification of Gene Products using Gene Ontology (GO) terms|Classification of Gene Products using Gene Ontology (GO) terms]].
+
===Expression Summary Ribbons===
  
−
The current release of GO data for all FlyBase genes can be found in the [http://{{flybaseorg}}/static_pages/downloads/current/go/gene_association.fb.gz gene_association.fb file]. The latest version of this data is available for download [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.fb.gz here] from the Gene Ontology consortium site. Details about the file format and comments on version differences can be found in the documentation on the [[FlyBase:Gene Ontology (GO) Annotation#Classification of Gene Products using Gene Ontology (GO) terms|Classification of Gene Products using Gene Ontology (GO) terms]].
+
The expression ribbons provide a graphical overview of expression data from three sources.
  
−
===Molecular Function===
+
====1. adult cell types - Fly Cell Atlas scRNA-seq====
 +
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene with dark red indicating the highest levels of expression. Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
  
−
A list of GO [http://geneontology.org/page/molecular-function-ontology-guidelines molecular function] terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided. The terms are divided into ''''Terms Based on Experimental Evidence'''' and ''''Terms Based on Predictions or Assertions''''.
 
  
−
'''CV term'''
+
Ribbon - FBbt mapping table:
  
−
Clicking on the term in the '''CV term''' column will take you to the relevant GO [[FlyBase:Controlled vocabularies used by FlyBase|CV Term Report]], which includes a definition of the GO term (where available).
+
{| class="wikitable" style="width: 100%;"
 +
|-
 +
! Tile Name
 +
! FBbt term
 +
! FBbt ID
 +
|-
 +
| neuron
 +
| neuron
 +
| FBbt:00005106
 +
|-
 +
| interneuron
 +
| interneuron
 +
| FBbt:00005125
 +
|-
 +
| motor neuron
 +
| motor neuron
 +
| FBbt:00005123
 +
|-
 +
| sensory neuron
 +
| sensory neuron
 +
| FBbt:00005124
 +
|-
 +
| sensory organ
 +
| cell sensory organ cell
 +
| FBbt:00005163
 +
|-
 +
| glial cell
 +
| glial cell
 +
| FBbt:00005144
 +
|-
 +
| muscle cell
 +
| muscle cell
 +
| FBbt:00005074
 +
|-
 +
| tendon cell
 +
| tendon cell
 +
| FBbt:00005090
 +
|-
 +
| epithelial cell
 +
| epithelial cell
 +
| FBbt:00000124
 +
|-
 +
| epidermal cell
 +
| epidermal cell
 +
| FBbt:00007325
 +
|-
 +
| Malpighian tubule cell
 +
| specialized Malpighian tubule cell
 +
| FBbt:00005794
 +
|-
 +
| nephrocyte
 +
| nephrocyte
 +
| FBbt:00047125
 +
|-
 +
| tracheocyte
 +
| tracheocyte
 +
| FBbt:00005038
 +
|-
 +
| fat cell
 +
| fat cell
 +
| FBbt:00046052
 +
|-
 +
| hemocyte
 +
| hemocyte
 +
| FBbt:00005063
 +
|-
 +
| oenocyte
 +
| oenocyte
 +
| FBbt:00004995
 +
|-
 +
| somatic precursor cell
 +
| somatic precursor cell
 +
| FBbt:00007008
 +
|-
 +
| somatic cell of ovariole
 +
| somatic cell of ovariole
 +
| FBbt:00006030
 +
|-
 +
| somatic cell of testis
 +
| somatic cell of testis
 +
| FBbt:00006031
 +
|-
 +
| female germline cell
 +
| female germline cell
 +
| FBbt:00057012
 +
|-
 +
| male germline cell
 +
| male germline cell
 +
| FBbt:00057011
 +
|-
 +
| male semen-secreting
 +
| cell semen-secreting cell of the male reproductive system
 +
| FBbt:00058293
 +
|-
 +
| other cell
 +
| type Any term that does not map to the above
 +
| Any ID that does not map to the above
 +
|}
  
−
GO CV terms may be preceded by qualifiers. The qualifier '''NOT''' is used to make an explicit note that the gene product is not associated with the GO term. The qualifier '''contributes_to''' is used when an individual gene product that is part of a complex can be annotated to terms that describe the function of the complex. contributes_to can only be used to qualify GO molecular function terms.
+
====2. anatomy - manually curated====
 +
Transcript and polypeptide expression data manually curated by FlyBase from individual publications is presented in a simple yes/no ribbon, in which the presence of curated data is marked by a colored tile. A colorless tile represents absence of manually curated data and can not be used to deduce the absence of expression. The ribbon is generated by using high-level summary categories to group expression curated using the [http://github.com/FlyBase/drosophila-anatomy-developmental-ontology Fly Anatomy Ontology (FBbt)].(See table below for mapping.)
 +
The complete data used to generate this ribbon can be viewed in the Transcript and Polypeptide sections below the ribbon section.
  
−
'''Evidence'''
+
Note that expression data from reporters is not used to populate the anatomy ribbon.
  
−
The type of evidence used to support the GO term is indicated in the evidence column. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology [http://geneontology.org/page/guide-go-evidence-codes Guide to GO Evidence Codes].
 
  
−
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the [http://www.geneontology.org/doc/GO.xrf_abbs GO.xrf_abbs] file. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
+
Ribbon - FBbt mapping table:
  
−
===Biological Process===
+
{| class="wikitable" style="width: 100%;"
−
 
+
|-
−
A list of GO [http://geneontology.org/page/biological-process-ontology-guidelines biological process] terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided. The terms are divided into ''''Terms Based on Experimental Evidence'''' and ''''Terms Based on Predictions or Assertions''''.
+
! Tile Name
−
 
+
! FBbt term(s)
−
'''CV term'''
+
! FBbt ID(s)
−
 
+
|-
−
Clicking on the term in the '''CV term''' column will take you to the relevant GO [[FlyBase:Controlled vocabularies used by FlyBase|CV Term Report]], which includes a definition of the term (where available).
+
| egg/oocyte
−
 
+
| egg, oocyte
−
GO CV terms may be preceded by qualifiers. The qualifier '''NOT''' is used to make an explicit note that the gene product is not associated with the GO term.
+
| FBbt:00000034, FBbt:00004886
−
 
+
|-
−
'''Evidence'''
+
| stem cell
−
 
+
| stem cell
−
The type of evidence used to support the GO term is indicated in the evidence column. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology [http://geneontology.org/page/guide-go-evidence-codes Guide to GO Evidence Codes].
+
| FBbt:00007014
−
 
+
|-
−
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the [http://www.geneontology.org/doc/GO.xrf_abbs GO.xrf_abbs] file. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
+
| imaginal tissue
 +
| imaginal tissue
 +
| FBbt:00047552
 +
|-
 +
| anlage/primordium
 +
| anlage, primordium
 +
| FBbt:00005426, FBbt:00005495
 +
|-
 +
| sensory system
 +
| sensory system, embryonic sensory system
 +
| FBbt:00007692, FBbt:00005827
 +
|-
 +
| nervous system
 +
| nervous system, presumptive embryonic/larval nervous system
 +
| FBbt:00005093, FBbt:00001055
 +
|-
 +
| circulatory system
 +
| circulatory system, presumptive embryonic/larval circulatory system
 +
| FBbt:00005057, FBbt:00005676
 +
|-
 +
| tracheal system
 +
| tracheal system, presumptive embryonic/larval tracheal system
 +
| FBbt:00005024, FBbt:00005569
 +
|-
 +
| digestive system
 +
| digestive system, presumptive embryonic/larval digestive system
 +
| FBbt:00005055, FBbt:00000438
 +
|-
 +
| adipose system
 +
| adipose system, presumptive embryonic/larval adipose system
 +
| FBbt:00005065, FBbt:00005708
 +
|-
 +
| endocrine system
 +
| endocrine system, presumptive embryonic/larval endocrine system
 +
| FBbt:00005068, FBbt:00005712
 +
|-
 +
| excretory system
 +
| excretory system
 +
| FBbt:00005056
 +
|-
 +
| reproductive system
 +
| reproductive system
 +
| FBbt:00004857
 +
|-
 +
| integumentary system
 +
| integumentary system, presumptive embryonic/larval integumentary system
 +
| FBbt:00004969, FBbt:00005392
 +
|-
 +
| muscle system
 +
| muscle system, presumptive embryonic/larval muscle system
 +
| FBbt:00005069, FBbt:00005647
 +
|-
 +
| other anatomical entity
 +
| Any term that does not map to the above
 +
| Any ID that does not map to the above
 +
|}
  
−
===Cellular Component===
+
====3. stages - modENCODE RNA-seq====
 +
High-throughput stage specific RNA-seq expression data is presented as a heat map, where a white tile represents no expression detected and the gradient range, from lowest to highest expression bin, is colored from yellow/green to red. This ribbon is a compressed version of the data from the modENCODE RNAseq project. Complete data can be viewed in the modENCODE Development RNA-Seq section under High-Throughput Expression.
  
−
A list of GO [http://geneontology.org/page/cellular-component-ontology-guidelines cellular component] terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided. The terms are divided into ''''Terms Based on Experimental Evidence'''' and ''''Terms Based on Predictions or Assertions''''.
+
===Testis-specificity index===
  
−
'''CV term'''
+
The testis-specificity index was calculated by [http://flybase.org/reports/FBrf0240104 Vedelek et al., 2018] from modENCODE tissue expression data. The scores indicate the degree of testis bias in expression and range from -2.52 (underrepresented) to 5.2 (very high testis bias).
−
 
 
−
Clicking on the term in the '''CV term''' column will take you to the relevant GO [[FlyBase:Controlled vocabularies used by FlyBase|CV Term Report]], which includes a definition of the term (where available).
 
−
 
 
−
GO CV terms may be preceded by the qualifiers. The qualifier '''NOT''' is used to make an explicit note that the gene product is not associated with the GO term. The qualifier colocalizes_with is used when a gene product is transiently or peripherally associated with an organelle or complex. It is also used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member. colocalizes_with can only be used to qualify GO cellular component CV terms.
 
−
 
 
−
'''Evidence'''
 
−
 
 
−
The type of evidence used to support the GO term is indicated in the evidence column. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] contains details of the evidence codes used by FlyBase.
 
−
 
 
−
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the [http://www.geneontology.org/doc/GO.xrf_abbs GO.xrf_abbs] file. The [[FlyBase:Gene Ontology (GO) Annotation##G.3.2. Evidence|evidence code documentation]] explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
 
−
==Expression Data==
 
  
 
===Transcript Expression===
 
===Transcript Expression===
Line 354: Line 746:
 
===High-Throughput Expression Data===
 
===High-Throughput Expression Data===
  
−
Associated Tools: Links to associated tools that enable visualization and searching of High-Throughput Expression Data
+
Associated Tools: Links to associated tools that enable visualization and searching of High-Throughput Expression Data<br>
 +
- [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2R%3A13437076..13452701&tracks=Gene_span%2CGene%2Ctopoview_modencode_30devstages&highlight= JBrowse]: view the gene's RNA-Seq signal across genomic regions.<br>
 +
- [http://flybase.org/static_pages/rna-seq/rna-seq_profile_search.html RNA-seq]: view expression profiles for each of the gene's exons across development or various tissues.<br>
  
−
View RNA-Seq signal across genomic region in [http://flybase.org/cgi-bin/gbrowse2/dmel/ GBrowse2].
+
Bulk Downloads: Download file of [[FlyBase:Downloads_Overview#RNA-Seq_RPKM_values_.28gene_rpkm_report_fb_.2A.tsv.gz.29|RNA-Seq RPK values]] for all genes.
  
−
'''RNA-Seq by Region'''
+
Reference: Reference for high-throughput expression data set.
−
 
 
−
View [http://flybase.org/static_pages/rna-seq/rna-seq_profile_search.html RNA-seq] expression profile for developmental stages.
 
−
 
 
−
View tissue-specific [http://flybase.org/static_pages/rna-seq/rna-seq_profile_search.html RNA-seq] expression profile.
 
−
 
 
−
 
 
−
Bulk Downloads - Download file of [[FlyBase:Downloads_Overview#RNA-Seq_RPKM_values_.28gene_rpkm_report_fb_.2A.tsv.gz.29|RNA-Seq RPK values]] for all genes.
 
−
 
 
−
Reference - Reference for high-throughput expression data set.
 
  
 
====FlyAtlas Anatomy Microarray====
 
====FlyAtlas Anatomy Microarray====
Line 379: Line 764:
  
  
−
'''modENCODE Anatomy RNA-Seq''' - see the [http://{{flybaseorg}}/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] dataset report for details.
+
''modENCODE Anatomy RNA-Seq'' - see the [http://{{flybaseorg}}/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] dataset report for details.
 +
 
 +
''modENCODE Development RNA-Seq'' - see the [http://{{flybaseorg}}/reports/FBlc0000206.html modENCODE_mRNA-Seq_tissues    ] dataset report for details.
 +
 
 +
''modENCODE Cell Lines RNA-Seq'' - see the [http://{{flybaseorg}}/reports/FBlc0000260.html modENCODE_mRNA-Seq_cell.B] dataset report for details.
  
−
'''modENCODE Development RNA-Seq''' - see the [http://{{flybaseorg}}/reports/FBlc0000206.html modENCODE_mRNA-Seq_tissues    ] dataset report for details.
+
''modENCODE Treatments RNA-Seq'' - see the [http://{{flybaseorg}}/reports/FBlc0000236.html modENCODE_mRNA-Seq_treatments] dataset report for details.
  
−
'''modENCODE Cell Lines RNA-Seq''' - see the [http://{{flybaseorg}}/reports/FBlc0000260.html modENCODE_mRNA-Seq_cell.B] dataset report for details.
+
''NIH Anatomical Expression RNA-Seq''' - expression levels for D. pseudoobscura genes from modENCODE RNA-Seq datasets: [http://{{flybaseorg}}/reports/FBlc0000599.html NIH_mRNA_Dpse_gonads_carcasses], [http://{{flybaseorg}}/reports/FBlc0000445.html NIH-Dpse_1_adult_heads] and [http://{{flybaseorg}}/reports/FBlc0000458.html NIH_mRNA_Dpse_2_adults].
  
−
'''modENCODE Treatments RNA-Seq''' - see the [http://{{flybaseorg}}/reports/FBlc0000236.html modENCODE_mRNA-Seq_treatments] dataset report for details.
+
====Developmental Proteome====
  
−
'''NIH Anatomical Expression RNA-Seq''' - expression levels for D. pseudoobscura genes from modENCODE RNA-Seq datasets: [http://{{flybaseorg}}/reports/FBlc0000599.html NIH_mRNA_Dpse_gonads_carcasses], [http://{{flybaseorg}}/reports/FBlc0000445.html NIH-Dpse_1_adult_heads] and [http://{{flybaseorg}}/reports/FBlc0000458.html NIH_mRNA_Dpse_2_adults].
+
Normalized, label-free quantitative (LFQ) protein expression was obtained from [http://{{flybaseorg}}/reports/FBrf0235991.html Casas-Vila et al., 2017] for about 8,000 protein coding genes. Expression values are sorted into one of seven expression level bins (from "at/below limit of detection" to "very high expression"). Expression values are presented as user-configurable histograms, color-coded by expression level bin. Expression values can be downloaded as a tab-separated values (.tsv) file. Links to the relevant dataset reports are at the top left of each section.
  
−
====Search for similarly expressed genes====
+
''Developmental Proteome: Embryogenesis'' - see the [http://{{flybaseorg}}/reports/FBlc0003385.html Casas-Vila_proteome_embryogenesis] dataset report for details.
  
−
This button will return genes with similar RNA-Seq expression patterns. It is currently offered only for the [http://flybase.org/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] developmental profile. Expression data comparisons were not generated by the modENCODE consortium but by FlyBase software. The 'search for similarly expressed genes' button on a gene report initiates a 'fixed' variant of a comparative search (using some fixed predefined search settings specific to expression).
+
''Developmental Proteome: Life Cycle'' - see the [http://{{flybaseorg}}/reports/FBlc0003384.html Casas-Vila_proteome_life_cycle] dataset report for details.
  
−
Searching is performed by comparison of gene expression level changes through the set of [similarly ordered] 'experiments' which represent known expression values under different experimental conditions (for staging data, experiments are the different developmental stages, for FlyAtlas data they are expression levels in different bodyparts/ tissues and so on). The purpose of the declared search is to compare sets of expression values from different genes, to determine the tendency of two datasets to vary together, in a somewhat correlated manner. The correlation coefficient is the best statistical test serving such a purpose.
+
====External Data and Images====
  
−
Predefined search settings (currently) include all developmental stages from modENCODE staging data. Sets of expression values from all genes are compared to the 'test' gene, resulting in an output of top matches. This is in the form of a custom HitList which includes graphical representation of the expression profiles. Visual inspection of these profiles might allow the user an idea about the interpretation of the obtained correlation (note, the 'test' gene profile in almost all cases is located at the top of the HitList as naturally, being compared to itself, it gives perfect 100% correlation match).
+
This section includes:
  
−
FlyBase provides a simple comparison tool for the modENCODE expression data. We hope this will aid the user in interpreting the expression patterns but we also appreciate that there are more complicated ways of comparing and interpreting the data.
+
Linkouts to external resources.
  
−
===Expression Clusters===
+
Expression pattern images.
−
This section reports co-expression clusters of which the gene is a member, based on RNA-Seq profiles of 30 developmental stages (see the [http://flybase.org/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] dataset report for details). These clusters were generated by two alternative clustering analyses from the modENCODE consortium. The first analysis by [http://flybase.org/reports/FBrf0213979.html The modENCODE Consortium et al., 2010] generated 34 clusters of 10,482 genes, as described in the [http://flybase.org/reports/FBlc0000358.html mE2_34_mRNA_expression_clusters] dataset report. The second analysis by [http://flybase.org/reports/FBrf0213980.html Graveley et al., 2011] generated 20 clusters of 11391 genes, as described in the [http://flybase.org/reports/FBlc0000393.html mE1_20_mRNA_expression_clusters] dataset report. Within a given analysis, genes could only be assigned to a single cluster (or none at all), but a gene may be part of one cluster from each of the two analyses. The report for each expression cluster lists all genes in that cluster (see the "Member" section).
 
  
−
==Alleles, Insertions, Transgenic Constructs and Phenotypes==
+
A link to the FlyBase wiki image resources page.
−
A series of tables containing classical and insertion alleles, transgenic constructs, aberrations and a summary of phenotypes. Allele symbols are hyperlinked to the corresponding [[FlyBase:Allele Report|Allele Report]] which contains more detailed information.
 
  
−
A camera thumbnail indicates that there is an image of the mutant phenotype for this allele. It is hyperlinked to the relevant section of [[FlyBase:Allele Report|Allele Report]].
+
==Alleles, Insertions and Transgenic Constructs==
 +
A series of tables containing classical and insertion alleles, transgenic constructs and aberrations relevant to the gene.
  
 +
''Documentation In Progress'' The tables in this section have recently been updated to give more flexibility when searching the genetic reagents that are available for your favorite gene. See this [https://{{flybaseorg}}/commentaries/2019_08/tooltables.html FlyBase Commentary] for more information.
  
 
===Classical and Insertion Alleles===  
 
===Classical and Insertion Alleles===  
 
The number in parentheses in the section header shows the total number of classical and insertion alleles that exist in FlyBase for this gene.
 
The number in parentheses in the section header shows the total number of classical and insertion alleles that exist in FlyBase for this gene.
  
−
A table listing all the classical and insertion alleles of the gene together with summary information:
+
A table listing all the classical and insertion alleles of the gene.
−
 
 
−
{| class= "wikitable"
 
−
!Column heading
 
−
!Description
 
−
|-
 
−
|'''Allele of <gene>'''
 
−
|Allele symbol. Click on this to go to the relevant [[FlyBase:Allele Report|Allele Report]].
 
−
|-
 
−
|'''Class'''
 
−
|[http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000286 Allele class] term that broadly describes the type of allele. Click on the term to go to the relevant [[FlyBase:Vocabularies|Term Report]].
 
−
|-
 
−
|'''Mutagen'''
 
−
|[http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000452 Mutagen] used to generate the allele. Clicking on the term to go to the relevant [[FlyBase:Vocabularies|Term Report]].
 
−
|-
 
−
|'''Associated Insertion'''
 
−
|Symbol of any insertion(s) associated with the allele, if applicable. Click on the symbol to go to the relevant [[FlyBase:Insertion Report|Insertion Report]].
 
−
|-
 
−
|'''Stocks'''
 
−
| Link to a hitlist of stocks from the public stock centers that contain this allele.
 
−
|-
 
−
|'''Known lesion'''
 
−
| 'Yes' if details of the lesion that causes the allele are known.
 
−
|-
 
−
|}
 
−
 
 
  
−
 
−
Click on the buttons at the top of this section to get either pre-selected data for all classical and insertion alleles, or to choose specific fields using the [http://{{flybaseorg}}/batchdownload Batch Download] tool.
 
  
 
====Other relevant insertions====
 
====Other relevant insertions====
−
A table showing other relevant insertions that affect the gene, subdivided into types of insertion. Each insertion type is only displayed on an individual '''Gene Report''' if it contains data.
+
A table showing other relevant insertions that affect the gene, either because the insertion maps within the transcription unit, and/or it has been shown to reflect the expression of the gene.
−
 
 
−
Types of insertion shown are:
 
−
 
 
−
 
 
−
{| class= "wikitable"
 
−
!Insertion type
 
−
!Description
 
−
|-
 
−
|'''insertion of mobile activating element'''
 
−
|The inserted element contains regulatory sequences that can activate expression of nearby endogenous loci.
 
−
|-
 
−
|'''insertion of enhancer trap'''
 
−
|The inserted element is an enhancer trap element.
 
−
|-
 
−
|'''insertion of enhancer trap binary system'''
 
−
|The inserted element is an enhancer trap element that encodes a driver that forms part of a binary expression system.
 
−
|-
 
−
|'''miscellaneous insertions'''
 
−
|The inserted element does not fall into any of the above categoriess
 
−
|-
 
−
|}
 
−
 
 
−
The table indicates whether expression data is available.
 
−
 
 
−
Clicking on the insertion symbol will take you to the relevant [[FlyBase:Insertion Report|Insertion Report]].
 
−
 
 
  
  
Line 478: Line 814:
 
====Transgenic constructs containing/affecting coding region of gene====
 
====Transgenic constructs containing/affecting coding region of gene====
  
−
A table listing all the transgenic constructs containing/affecting the coding region of the gene, together with summary information:
+
A table listing all the transgenic constructs containing/affecting the coding region of the gene.
  
  
−
{| class= "wikitable"
 
−
!Column heading
 
−
!Description
 
−
|-
 
−
|'''Allele of <gene>'''
 
−
|Allele symbol. Click on this to go to the relevant [[FlyBase:Allele Report|Allele Report]].
 
−
|-
 
−
|'''Mutagen'''
 
−
|[http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0000452 Mutagen] used to generate the allele. Clicking on the term to go to the relevant [[FlyBase:Vocabularies|Term Report]].
 
−
|-
 
−
|'''Associated Transgenic Construct'''
 
−
|Transgenic construct symbol. Click on this to go to the relevant [[FlyBase:Recombinant_Construct_Report|Recombinant Construct Report]].
 
−
|-
 
−
|'''Stocks'''
 
−
|Link to a hitlist of stocks from the public stock centers that contain an insertion of this transgenic construct.
 
−
|-
 
−
|}
 
  
 +
====Transgenic constructs containing regulatory region of gene====
  
−
Click on the buttons at the top of this section to get either pre-selected data for all alleles carried on transgenic constructs, or to choose specific fields using the [http://{{flybaseorg}}/static_pages/downloads/ID.html Batch Download] tool.
+
A table showing transgenic constructs containing the regulatory region of the gene.
−
 
 
−
====Transgenic constructs regulatory region region of gene====
 
−
 
 
−
A table showing transgenic constructs containing the regulatory region of the gene, subdivided by the type of construct. Each constructs type is only displayed on an individual '''Gene Report''' if it contains data.
 
−
 
 
−
Types of constructs shown are:
 
−
 
 
−
{| class= "wikitable"
 
−
!Construct type
 
−
!Description
 
−
|-
 
−
|'''reporter construct'''
 
−
|Construct encodes a reporter (e.g. lacZ).
 
−
|-
 
−
|'''vital-reporter construct'''
 
−
|Construct encodes a fluorescent reporter (e.g. GFP).
 
−
|-
 
−
|'''GAL4 construct'''
 
−
|Construct encodes a GAL4 driver.
 
−
|-
 
−
|}
 
−
 
 
  
−
Clicking on the transgenic construct symbol will take you to the relevant [[FlyBase:Recombinant Construct Report|Recombinant Construct Report]].
 
  
−
The table indicates whether expression data is available.
 
  
−
===Deletions and Duplications===
+
===Aberrations (Deficiencies and Duplications)===
  
 
The number in parentheses in the section header show the total number of deletions and duplications  
 
The number in parentheses in the section header show the total number of deletions and duplications  
Line 534: Line 830:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Disrupted in'''    || style="width: 80%;" | A list of aberrations that have been reported to completely delete/disrupt the gene, determined by either complementation or molecular analysis.
+
|'''Gene disrupted in'''    || style="width: 80%;" | A list of aberrations that have been reported to completely delete/disrupt the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 540: Line 836:
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
|-
 
|-
−
|'''Partially disrupted in'''    || A list of aberrations that have been reported to partially disrupt the gene, determined by either complementation or molecular analysis.
+
|'''Gene partially disrupted in'''    || A list of aberrations that have been reported to partially disrupt the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 546: Line 842:
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
|-
 
|-
−
|'''Not Disrupted in'''    || A list of aberrations that have been reported not to disrupt the gene, determined by either complementation or molecular analysis.
+
|'''Gene not Disrupted in'''    || A list of aberrations that have been reported not to disrupt the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 552: Line 848:
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
|-
 
|-
−
|'''Duplicated in'''    || A list of aberrations that have been reported to completely duplicate the gene, determined by either complementation or molecular analysis.
+
|'''Gene duplicated in'''    || A list of aberrations that have been reported to completely duplicate the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 558: Line 854:
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
|-
 
|-
−
|'''Partially duplicated in'''    || A list of aberrations that have been reported to partially duplicate the gene, determined by either complementation or molecular analysis.
+
|'''Gene partially duplicated in'''    || A list of aberrations that have been reported to partially duplicate the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 564: Line 860:
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
This field is only displayed in an individual '''Gene Report''' if it contains data.
 
|-
 
|-
−
|'''Not duplicated in'''    || A list of aberrations that have been reported not to duplicate the gene, determined by either complementation or molecular analysis.
+
|'''Gene not duplicated in'''    || A list of aberrations that have been reported not to duplicate the gene, determined by either complementation or molecular analysis.
  
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
 
Clicking on an aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].
Line 571: Line 867:
 
|}
 
|}
  
−
===Summary of Allele Phenotypes===
+
==Variants==
 +
 
 +
{| class="wikitable" style="width: 100%;"
 +
|'''Variant Molecular Consequences''' || Variants data from FlyBase are run through the Ensembl [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4 VEP] (Variant Effect Predictor) pipeline, and the results are displayed in a scrolling table. The VEP algorithm considers the genomic location, mutation type, and nucleotide change of a variant to calculate the molecular consequence on all of the overlapping transcripts affected by the variant. In addition to reporting the molecular change to the transcripts and encoded CDS, it assigns a Sequence Ontology (SO)-based consequence term to each variant/transcript combination.
 +
 
 +
The table displays, for each variant, all genes that are potentially affected by that variant, any alleles of those genes associated with the variant, and the predicted consequences to all affected transcripts. The gene that is the subject of the report is highlighted in the table.
 +
 
 +
This is the result of a collaboration between FlyBase, [https://www.alliancegenome.org/ Alliance of Genome Resources] and Ensembl.
 +
|-
 +
|'''Alleles Representing Disease-Implicated Variants''' || A table showing mutants or transgenic alleles that have been used as models for a human disease. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model.
 +
 
 +
The results are shown in an interactive table with columns for allele, human variant designation, human variant synonyms, external links, human disease model, the originating reference, the number of references associated with the allele, and comments.
 +
 
 +
The tables have many features to optimize usability, including pagination for very large lists, row filtering by column (click on the column heading), row sorting by column (insert search term in the Filer... box), the ability to hide/show individual columns (access from button at upper right corner of table), column reordering (click and drag the column header), and the ability to export to a Hitlist, CSV, or Excel (button at upper left corner of table).
 +
|-
 +
|}
 +
 
 +
==Phenotypes==  
  
 
A table containing a summary of the phenotypes of alleles of the gene. The table lists [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] terms describing the phenotype, together with the allele(s) of the gene which have been reported to show this phenotype.
 
A table containing a summary of the phenotypes of alleles of the gene. The table lists [[FlyBase:Controlled vocabularies used by FlyBase|controlled vocabulary]] terms describing the phenotype, together with the allele(s) of the gene which have been reported to show this phenotype.
Line 598: Line 911:
  
 
==Orthologs==
 
==Orthologs==
−
The orthologs section presents orthology calls between D. melanogaster and other species provided by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] for human and 7 model organism species and [http://orthodb.org/ OrthoDB] for other species. The complete set of orthology calls for  DIOPT and OrthoDB can be downloaded using the buttons at the top of the section and for the subsections via the download thumbnails in the subsection header bar.
+
The orthologs section presents orthology calls between D. melanogaster and other species provided by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] for human and model organism species and [http://orthodb.org/ OrthoDB] for other species. The complete set of orthology calls for  DIOPT can be downloaded using the buttons at the top of the section and for the subsections via the download thumbnails in the subsection header bar.
 +
 
 
===Human Orthologs (via DIOPT)===
 
===Human Orthologs (via DIOPT)===
  
Line 610: Line 924:
 
* '''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")
 
* '''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")
 
* '''Alignment''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
 
* '''Alignment''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
−
* '''Transgene in Fly''': Where applicable, a link to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila
+
* '''Complementation?''': Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been show to functionally complement the Dmel gene
 +
* '''Transgene?''': Where applicable, a link in the form of a Drosophila icon to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila
  
 
===Model Organism Orthologs (via DIOPT)===
 
===Model Organism Orthologs (via DIOPT)===
  
−
This section presents orthology calls between D. melanogaster and 7 other model organisms: Rattus norvegicus (Norway rat), Mus musculus (laboratory mouse), Xenopus tropicalis (Western clawed frog), Danio rerio (zebrafish), Caenorhabditis elegans (nematode, roundworm), Saccharomyces cerevisiae (brewer's yeast) and Schizosaccharomyces pombe (fission yeast)), as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)]. The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].)
+
This section presents orthology calls between D. melanogaster and other model organisms, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)]. The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].)
  
 
The list of ortholog predictions is arranged by species, in order of increasing phylogenetic distance relative to human.
 
The list of ortholog predictions is arranged by species, in order of increasing phylogenetic distance relative to human.
Line 621: Line 936:
 
* '''Species\Gene Symbol''': official gene symbol, as used in (and linked to) the relevant model organism database, prefixed with the [http://flybase.org/wiki/FlyBase:Abbreviations 4-letter species abbreviation] used in FlyBase
 
* '''Species\Gene Symbol''': official gene symbol, as used in (and linked to) the relevant model organism database, prefixed with the [http://flybase.org/wiki/FlyBase:Abbreviations 4-letter species abbreviation] used in FlyBase
 
The NBCI thumbnail links to the gene report page at NCBI.
 
The NBCI thumbnail links to the gene report page at NCBI.
 +
* '''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")
 
* '''Best Score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
 
* '''Best Score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
 
* '''Best Rev Score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
 
* '''Best Rev Score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
 
* '''Source''': check-boxes indicating which individual ortholog prediction tools support a given orthologous gene-pair relationship
 
* '''Source''': check-boxes indicating which individual ortholog prediction tools support a given orthologous gene-pair relationship
−
* '''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")
 
 
* '''Alignment''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
 
* '''Alignment''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
−
* '''Transgene in Fly''': Where applicable, a link to a FlyBase Gene Report for the orthologous gene, indicating that it has been expressed transgenically in Drosophila
+
* '''Complementation?''': Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been shown to functionally complement the D. melanogaster gene
 +
* '''Transgene?''': Where applicable, a link in the form of a Drosophila icon to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila
  
−
===Orthologs (via OrthoDB)===
+
===Other Organism Orthologs (via OrthoDB)===
  
−
This section presents a uniform set of [http://orthodb.org/ OrthoDB]-derived orthology calls between D. melanogaster and around 40 other species, biased towards those closely related to D. melanogaster. Orthology calls are arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, and non-Arthropod Metazoa.
+
This section presents [http://orthodb.org/ OrthoDB]-derived orthology calls between D. melanogaster and other metazoa not included in the DIOPT orthology set, including other Drosophila species, dipterans, insects and arthropods. These data are retrieved directly from OrthoDB via API calls and therefore reflect the current OrthoDB version (which can be checked by clicking on the 'OrthoDB' link at the top of the section).
  
−
A link to OrthoDB for each of the 5 groups is provided in the each subsection header. Below this are separate sections for each orthology group listing the relevant predicted orthologs. The groups, and the species within them, are listed in order of increasing phylogenetic distance relative to D. melanogaster.
+
The columns are:
−
 
 
−
The columns in each section are:
 
 
* '''Organism''': the latin species designation
 
* '''Organism''': the latin species designation
−
* '''Common Name''': the common species name
+
* '''Common Name''': the common species name (when available)
−
* '''Gene''':  symbol/ID of the orthologous gene, linked to an appropriate species database or [http://www.ensembl.org/ Ensembl], prefixed with the [http://flybase.org/wiki/FlyBase:Abbreviations 4-letter species abbreviation] used in FlyBase
+
* '''Gene ID''':  symbol/ID of the orthologous gene, linked to the gene report at OrthoDB
−
* '''AAA Syntenic Ortholog''': (only shown for the ‘Drosophila species’ group)
+
* '''OrthoDB description''': name/description of the orthologous gene
−
* '''Multiple Dmel Genes in this Orthologous Group''': either blank or ‘Y’, as appropriate
 
  
−
For non-D. melanogaster FlyBase gene reports, the Orthologs sections includes links to the OrthoDB Ortholog groups (if any are identified) as well as a link to the orthologous D. melanogaster gene (where one has been identified).
+
==Paralogs==
 +
The paralogs section presents paralogy calls within D. melanogaster as provided by [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)]. The DIOPT approach integrates paralog predictions from multiple tools, thereby giving an overview of potential paralogs derived from different algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].)
  
 +
The complete set of paralogy calls can be downloaded using the button at the top of the section.
  
 +
The columns on the main table are:
 +
* '''Gene Symbol''': the FlyBase gene symbol. The NBCI thumbnail links to the gene report page at NCBI.
 +
* '''Score''':  the number of tools that support a given paralogous gene-pair relationship compared to the total number of tools that compute paralogy relationships (expressed as "X of Y")
 +
* '''Source''': check-boxes indicating which individual prediction tools support a given gene-pair relationship
 +
* '''Alignment''': link to an alignment between the given gene-pairs on the DIOPT site
  
−
==Human Disease Model Data==
+
==Human Disease Associations==
  
 
===FlyBase Human Disease Model Reports===
 
===FlyBase Human Disease Model Reports===
Line 651: Line 971:
 
Links to [[FlyBase:Human_Disease_Report|Human Disease Model Reports]] associated with this gene.
 
Links to [[FlyBase:Human_Disease_Report|Human Disease Model Reports]] associated with this gene.
  
−
===Alleles Reported to Model Human Disease (Disease Ontology)===
+
 
 +
===Disease Model Summary Ribbon===
 +
 
 +
This ribbon summarizes Disease Ontology annotations for disease models in FlyBase, as given in the "Models Based on Experimental Evidence" and "Potential Models Based on Orthology" subsections below.  (Modifier and negative annotations are excluded.)  The ribbon is broken into broad categories of infection, anatomical entity, proliferation and other diseases, and is analogous to the equivalent ribbon used at the [https://www.alliancegenome.org Alliance of Genome Resources].
 +
 
 +
===Disease Ontology (DO) Annotations===
  
 
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology].
 
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology].
Line 657: Line 982:
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''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.
+
|'''Models Based on Experimental Evidence''' || 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.
  
−
The table consists of four columns
+
The table consists of four columns:
  
 
'''Allele''' - The alleles of the gene that is being used as a model.
 
'''Allele''' - The alleles of the gene that is being used as a model.
Line 665: Line 990:
 
'''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]).
 
'''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]).
  
−
'''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.
+
'''Evidence''' - '''CEA''' (combinatorial experimental and author inference evidence used in manual assertion; ECO:0007013) is used when an annotation is made based on experimental evidence AND the disease term used agrees with that stated by the authors. This is the most commonly used evidence code.  '''CEC''' (combinatorial experimental and curator inference evidence used in manual assertion; ECO:0007014) is used when an annotation is made based on experimental evidence BUT the disease term used has been determined by a curator rather than based on a statement by the authors of the paper.  Use of this evidence code is relatively rare, restricted to cases where (i) the disease stated by the authors is relatively general (e.g. “amyotrophic lateral sclerosis”), but the curator can provide a more specific subtype (e.g. “amyotrophic lateral sclerosis type 6”) based on the given human gene/variant and its known relationship to a specific disease (e.g. in OMIM); or (ii) the authors have made a mistake in the given gene-to-disease relationship.  If the given allele only models the disease in combination with another allele, the word '''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.
  
 
'''References''' - lists the reference(s) that describe the model.
 
'''References''' - lists the reference(s) that describe the model.
Line 671: Line 996:
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
  
−
The information displayed in this table can be downloaded using the button at the top of the section.
+
The information displayed in this table can be downloaded using the 'Models Data' button at the top of the section.
 
|-
 
|-
−
|'''Interactions''' || A table showing interactions of this allele with other disease-causing allele(s)
+
|'''Potential Models Based on Orthology''' || style="width: 80%;" | A table showing any disease(s) that are associated with the human ortholog of the given D. melanogaster gene.
  
−
The table consists of four columns
+
The table consists of four columns:
 +
 
 +
'''Human Ortholog''' - the human gene orthologous to the given D. melanogaster gene
 +
 
 +
'''Disease''' - the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]) associated with that human gene, as annotated in [https://www.omim.org OMIM]
 +
 
 +
'''Evidence''' - this is always 'inferred from electronic annotation'
 +
 
 +
'''References''' - lists the reference ([http://flybase.org/reports/FBrf0241599.html FBrf0241599]) describing the logic of this orthology-based algorithm.
 +
 
 +
|-
 +
|'''Modifiers Based on Experimental Evidence''' || A table showing interactions of this allele with other disease-causing allele(s)
 +
 
 +
The table consists of four columns:
  
 
'''Allele''' - The alleles of the gene that is being used as a model.
 
'''Allele''' - The alleles of the gene that is being used as a model.
Line 687: Line 1,025:
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
 
|-
 
|-
−
|'''Comments''' || Curated comments that highlight certain features of a model, for example, when particular aspects of a disease phenotype are modeled while others are not. These comments are used sparingly to avoid duplication with phenotype information.
+
|'''Comments on Models/Modifiers Based on Experimental Evidence''' || Curated comments that highlight certain features of a model, for example, when particular aspects of a disease phenotype are modeled while others are not. These comments are used sparingly to avoid duplication with phenotype information.
  
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
 
This information is also shown on the individual [[FlyBase:Allele Report|allele reports]].
  
−
The information displayed in this table can be downloaded using the button at the top of the section.
+
The information displayed in this table can be downloaded using the 'Interactions Data' button at the top of the section.
 
|}
 
|}
  
−
===Human Orthologs (via DIOPT)===
+
===Human Orthologs (via DIOPT) and Disease Associations===
 
Orthology calls between D. melanogaster and human, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)], together with links to relevant gene and phenotype reports at the [http://omim.org/ Online Mendelian Inheritance in Man (OMIM)] database. The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].)
 
Orthology calls between D. melanogaster and human, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)], together with links to relevant gene and phenotype reports at the [http://omim.org/ Online Mendelian Inheritance in Man (OMIM)] database. The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].)
  
Line 702: Line 1,040:
 
* '''Gene Name''': the official human gene symbol and name, as used at (and linked to) the [http://www.genenames.org/ HGNC]
 
* '''Gene Name''': the official human gene symbol and name, as used at (and linked to) the [http://www.genenames.org/ HGNC]
 
* '''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")
 
* '''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")
−
* '''OMIM ID''': the [http://omim.org/ OMIM] number for this human gene, linked to the corresponding OMIM gene report
+
* '''OMIM''': the [http://omim.org/ OMIM] number for this human gene, linked to the corresponding OMIM gene report
 
* '''OMIM Phenotype''': any phenotypes associated with the human gene, as reported in [http://omim.org/ OMIM], and linked to the corresponding OMIM phenotype report
 
* '''OMIM Phenotype''': any phenotypes associated with the human gene, as reported in [http://omim.org/ OMIM], and linked to the corresponding OMIM phenotype report
 +
* '''DO Term''':  The [http://disease-ontology.org Disease Ontology] term equivalent to the given OMIM term, as determined by the OMIM cross-references within the DO.
 +
* '''Complementation''': Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been show to functionally complement the D. melanogaster gene
 
* '''Transgene in Fly''': Where applicable, a link to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila
 
* '''Transgene in Fly''': Where applicable, a link to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila
  
−
==Interactions and Pathways==
+
==Functional Complementation Data==
 +
 
 +
This section 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 table shows 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.
 +
 
 +
The columns are:
 +
 
 +
* '''Dmel gene''': current FlyBase symbol of Dmel gene
 +
 
 +
* '''Ortholog showing functional complementation''': 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.
 +
 
 +
* '''Supporting References''': list of publications that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog.
 +
 
 +
==Interactions==
  
 
===Summary of Physical Interactions===
 
===Summary of Physical Interactions===
Line 743: Line 1,095:
 
Clicking on a reference will take you to the relevant '''Reference Report'''.
 
Clicking on a reference will take you to the relevant '''Reference Report'''.
  
 +
==Pathways==
  
 +
===Signaling Pathways (FlyBase) ===
 +
Where relevant, this section gives a link to, and description of, any signaling pathway in which the given gene (product) is involved, as curated by FlyBase. (A list of currently curated pathways is [http://flybase.org/lists/FBgg/pathways here].)
 +
 +
===Metabolic Pathways===
 +
This section shows link-outs to several different metabolic pathway resources(including [https://www.genome.jp/kegg/pathway.html KEGG Pathway], [https://reactome.org Reactome] and [https://biocyc.org/ BioCyc]) that include the gene (product) within the given metabolic pathway or process.
 +
 +
===External Data===
 +
This section shows link-outs to several different pathway resources (including [https://www.genome.jp/kegg/pathway.html KEGG Pathway], [https://reactome.org Reactome] and [http://signalink.org SignaLink]) that include the gene (product) within the given signaling pathway or other process.
  
 
==Genomic Location and Detailed Mapping Data==
 
==Genomic Location and Detailed Mapping Data==
Line 755: Line 1,116:
 
See  [[FlyBase:Computed_cytological_data|Computed cytological data]] in FlyBase for a detailed description of how this computed cytological location is calculated.
 
See  [[FlyBase:Computed_cytological_data|Computed cytological data]] in FlyBase for a detailed description of how this computed cytological location is calculated.
 
|-
 
|-
−
|'''Recombination map'''    || A computed genetic map position for the gene, derived from the full list of terms listed in the '''Experimentally Determines Recombination Data''' subsection.
+
|'''Recombination map'''    || A computed genetic map position for the gene, derived from the full list of terms listed in the '''Experimentally Determined Recombination Data''' subsection.
  
−
The genetic map position is given as chromosome number-map position, or simply chromosome number-, if the gene has not been mapped within the chromosome.
+
The genetic map position is given as chromosome number-map position, or simply chromosome number, if the gene has not been mapped within the chromosome.
 
|-
 
|-
 
|'''Sequence location'''    || The extent of the transcription unit on the genome, prefixed with the chromosome arm that the gene is located on. The strand to which the gene maps is indicated in square brackets after the sequence coordinates.
 
|'''Sequence location'''    || The extent of the transcription unit on the genome, prefixed with the chromosome arm that the gene is located on. The strand to which the gene maps is indicated in square brackets after the sequence coordinates.
Line 782: Line 1,143:
 
If a gene has been mapped cytogenetically but not genetically, an estimated genetic position may be given in square brackets, inferred from a standard Map Conversion Table.
 
If a gene has been mapped cytogenetically but not genetically, an estimated genetic position may be given in square brackets, inferred from a standard Map Conversion Table.
  
−
==Stocks & Reagents==
+
==Stocks and Reagents==
  
−
===Stocks Listed in FlyBase===
+
===Stocks===
  
−
A list of the stocks from the public stocks centers that contain this gene; genotypes may be provided. If there are a large number of such stocks, the list may be truncated. For participating stock centers, clicking on the stock number will take you to the appropriate stock report.
+
A list of the stocks from the public stocks centers that contain this gene; genotypes may be provided. The number of stocks is indicated in parentheses. If there are a large number of stocks, the list may be truncated. Click on the 'More stocks available' button to show all in a FlyBase HitList. For participating stock centers, clicking on the stock number will take you to the appropriate stock report.
  
 
===Genomic Clones===
 
===Genomic Clones===
  
−
A list of genomic clones that are associated with this gene.
+
A list of genomic clones that are associated with this gene. The number of genomic clones is indicated in parentheses. Clicking on the 'List GenBank IDs' button generates a table of genomic clones related to the gene with links to GenBank records.
 +
 
 +
Note: FlyBase no longer curates genomic clone accessions so this list may not be complete.
  
 
===cDNA Clones===
 
===cDNA Clones===
  
−
This section lists cDNA clones that have been associated with this gene. It is subdivided to distinguish fully sequenced clones from those which have only been partially characterized. Clones that are part of the BDGP DGC collection are listed separately from the other clones.
+
This section lists cDNA clones that have been associated with this gene. The number of cDNA clones is indicated in parentheses. It is subdivided to distinguish fully sequenced clones from those which have only been partially characterized. Clones that are part of the BDGP DGC collection are listed separately from the other clones.
  
 
These associations are primarily automated and at this time include clones containing inserts that support the gene model as well as clones containing inserts that overlap the gene model but do not support any of the currently annotated transcripts. Efforts have been made to eliminate from this list clones that overlap the gene model but support another gene model in the same genomic region (i.e. a gene nested within an intron of another gene). In addition, clones containing sequences that overlap transposable elements have been excluded from this list.
 
These associations are primarily automated and at this time include clones containing inserts that support the gene model as well as clones containing inserts that overlap the gene model but do not support any of the currently annotated transcripts. Efforts have been made to eliminate from this list clones that overlap the gene model but support another gene model in the same genomic region (i.e. a gene nested within an intron of another gene). In addition, clones containing sequences that overlap transposable elements have been excluded from this list.
Line 802: Line 1,165:
 
===RNAi & Array Information===
 
===RNAi & Array Information===
  
−
Linkouts to RNAi and array resources. Clicking on the linkout identifier will take you to the appropriate entry in the external database from which they are derived.
+
Linkouts to RNAi and array resources. Clicking on the linkout identifier will take you to the appropriate clone report entry in the external database from which they are derived.
  
 
Resources currently listed include
 
Resources currently listed include
  
 +
[https://fgr.hms.harvard.edu/ DRSC]
  
−
DRSC
+
[http://www.genomernai.org/ GenomeRNAi]
−
 
 
−
GenomeRNAi
 
  
 
===Antibody Information===
 
===Antibody Information===
  
−
A list of publications in which the generation of antibodies against the subject polypeptide has been reported. Each entry is categorized as "polyclonal" or "monoclonal" to indicate the nature of the antibodies. In cases where a monoclonal antibody is available from the Developmental Studies Hybridoma Bank in Iowa, a link the DSHB website is provided.
+
A list of publications in which the generation of antibodies against the subject polypeptide has been reported. Each entry is categorized as "polyclonal" or "monoclonal" to indicate the nature of the antibodies. In cases where a monoclonal antibody is available from the Developmental Studies Hybridoma Bank in Iowa, a link to the DSHB website is provided in the '''Commercially Available Antibodies''' section.
  
−
==Other Information==
+
FlyBase also lists [[FlyBase:Antibodies|antibody resources]].
  
−
===Relationship to Other Genes===
+
===Cell Line Information===
  
 
{| class="wikitable" style="width: 100%;"
 
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Source for database identity of''' || style="width: 80%;" | A statement indicating that the valid symbol used in FlyBase for the gene has been changed, because it previously had an arbitrary symbol, for example a gene that was identified by genomic sequencing projects e.g. CG8896, or was a lethal locus named solely by its cytogenetic location, e.g. l(3)64Aj. The publication that was the source of the change is listed.
+
|Publicly Available Cell Lines || style="width: 80%;" | Links to FlyBase reports for cell lines available from the Drosophila Genomics Resource Center or commercial sources
 +
|-
 +
|Other Stable Cell Lines || Contains comments about stable cell lines reported in publications that were generated to study a gene via knockout, over-expression, tagging or some other method.
 +
|}
  
−
The statement consists of the new symbol and previously used symbol of the gene at the time of the rename, prefixed with "Source for identity of: "
+
==Other Comments==
  
−
See Gene symbols and names in the nomenclature document for cases when renaming may occur.
+
Miscellaneous free text comments about the gene.
 +
 
 +
==Relationship to Other Genes==
 +
 
 +
{| class="wikitable" style="width: 100%;"
 
|-
 
|-
−
|'''Source for database merge of''' || A statement indicating that two (or more) gene records have been merged into a single gene record in the database, together with the publication that was the source of the merge.
+
|'''Source for database merge of''' || A statement indicating that two (or more) gene records have been merged into a single gene record. The statement consists of the valid symbols of the genes at the time of the merge, prefixed with "Source for merge of: ", followed by the publication that was the source of the merge.
−
 
 
−
The statement consists of the valid symbols of the gene at the time of the merge, prefixed with "Source for merge of: "
 
 
|-
 
|-
 
|'''Member gene of''' || If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
 
|'''Member gene of''' || If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
  
−
This field is displayed in the Gene Report for the individual member of the cluster and lists the gene symbol of the generic record, representing the whole cluster, that the gene is a member of.
+
This field is displayed in the Gene Report for the individual member of the cluster and lists the gene symbol of the generic record, representing the whole cluster, that the gene is a member of. Clicking on the gene symbol will take you to the '''Gene Report''' for the generic record representing the whole cluster.
−
 
 
−
Clicking on the gene symbol will take you to the '''Gene Report''' for the generic record representing the whole cluster.
 
  
 
This field is only displayed in an individual Gene Report if it contains data.
 
This field is only displayed in an individual Gene Report if it contains data.
Line 841: Line 1,206:
 
|'''Component gene(s)''' || If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
 
|'''Component gene(s)''' || If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
  
−
This field is displayed in the Gene Report for the generic record, representing the whole cluster, and lists the gene symbols of the individual members of the cluster.
+
This field is displayed in the Gene Report for the generic record, representing the whole cluster, and lists the gene symbols of the individual members of the cluster. Clicking on a gene symbol will take you to the '''Gene Report''' for individual member of the cluster.
  
−
Clicking on a gene symbol will take you to the '''Gene Report''' for individual member of the cluster.
+
This field is only displayed in an individual Gene Report if it contains data.
 +
|-
 +
|'''Encoded by''' || This field is typically displayed in a Gene Report for genes encoded by natural transposons, and lists the symbol of the natural transposon that encodes the gene. Clicking on the symbol will take you to the '''Report''' for the natural transposon.
  
 
This field is only displayed in an individual Gene Report if it contains data.
 
This field is only displayed in an individual Gene Report if it contains data.
 
|-
 
|-
−
|'''Encoded by''' || This field is typically displayed in a Gene Report for genes encoded by natural transposons, and lists the symbol of the natural transposon that encodes the gene.
+
|'''Additional comments''' || Free text comments about the relationship of the gene to other genes or groups of alleles.
 +
|}
  
−
Clicking on the symbol will take you to the '''Report''' for the natural transposon.
+
==Nomenclature History==
  
−
This field is only displayed in an individual Gene Report if it contains data.
+
{| class="wikitable" style="width: 100%;"
 +
|-
 +
|'''Source for database identity of''' || style="width: 80%;" | A statement indicating that the symbol used in FlyBase for the gene has been changed. The statement consists of the new symbol and previously used symbol of the gene at the time of the rename, prefixed with "Source for identity of: ", followed by the publication that was the source of the change.
 +
|-
 +
|'''Nomenclature comments''' || style="width: 80%;" | Explanation for changing the symbol/name of a previously named gene, such as a change based on the preferred usage by the community, rationalizing nomenclature within a gene family, or because a symbol/name contravenes our nomenclature rules. Such changes are usually actioned directly by FlyBase, though may be the result of information in a publication (e.g. paper or personal communication).
 
|-
 
|-
−
|'''Tags''' || This field is displayed in a Gene Report that represents an engineered tag that has been used in a transgenic construct to mark genes or their products. This includes epitope tags such as "Avic\GFP" and function tags such as nuclear localization signals.
+
|'''Etymology''' || style="width: 80%;" | The explanation behind the gene name as reported by the authors.
 +
|}
  
−
The field lists the alleles that contain the tag.
+
==Synonyms & Secondary IDs==
  
−
Clicking on the symbol will take you to the relevant '''Allele Report'''.
+
===Reported As===
  
−
This field is only displayed in an individual Gene Report if it contains data.
+
{| class="wikitable" style="width: 100%;"
 +
|-
 +
|'''Symbol Synonym''' || style="width: 80%;" | A list of symbols that have been used in the literature, or by FlyBase, to describe the gene.
 
|-
 
|-
−
|'''Additional comments''' || Free text comments about the relationship of the gene to other genes or groups of alleles.
+
|'''Name Synonym''' || A list of names that have been used in the literature, or by FlyBase, to describe the gene.
 
|}
 
|}
  
−
===Other Comments===
+
===Secondary FlyBase IDs===
  
−
Miscellaneous free text comments about the gene.
+
A list of Secondary FlyBase identifier numbers of the gene.
  
−
===Origin and Etymology===
+
If a gene has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.
  
−
====Discoverer====
+
==Datasets==
  
−
A list of the individuals who identified the gene.
+
A list of datasets in which the gene was either a key experimental variable, or in which the gene was a key result.
  
−
====Etymology====
+
===Study focus===
 +
Datasets in which the gene was a key experimental variable.
  
−
The explanation behind the gene name as reported by the authors.
+
{| class= "wikitable"
 +
!Column heading
 +
!Description
 +
|-
 +
|'''Experimental Role'''
 +
|How the gene was involved in the experimental design. For example, the gene may have been an "RNAi_target", or its product may have been a "bait_protein" for some ChIP study.
 +
|-
 +
|'''Project'''
 +
|The name of the project (dataset), which links to the FlyBase "project" report (more detailed reports for related biosamples, assays and results therein).
 +
|-
 +
|'''Project Type'''
 +
|The type of project. For example, [http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0003033 "genome binding"] or [http://{{flybaseorg}}/cgi-bin/cvreport.pl?cvterm=FBcv:0003034 "transcriptome"]
 +
|-
 +
|'''Title'''
 +
|The project's title, which provides a very short description of the study.
 +
|-
 +
|}
  
−
====Identification====
+
===Study result===
−
 
+
Coming soon. This section will document studies in which the gene is a key "hit" in some screen or analysis.
−
Details of how the gene was identified.
 
  
 
==External Crossreferences & Linkouts==
 
==External Crossreferences & Linkouts==
  
−
A complete list of links to external databases for the gene. These links may also be present in other sections of the Gene Report, where appropriate. The '''SEQUENCE CROSSREFERENCES''' and '''OTHER CROSSREFERENCES''' sections contain accession numbers which are FlyBase curated links. The '''LINKOUTS''' section contains Linkouts. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
+
A list of links to external databases for the gene. These links may also be present in other sections of the Gene Report, where appropriate. The '''Sequence Crossreferences''' and '''Other Crossreferences''' sections contain accession numbers which are FlyBase curated links. The '''Linkouts''' section contains linkouts to other relevant resources. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
  
−
The '''SEQUENCE CROSSREFERENCES''' section contains accession numbers from the following databases:
+
The '''Sequence Crossreferences''' section contains accession numbers from the following databases:
  
  
−
DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe
+
NCBI Gene - Integrated gene report at NCBI
  
−
UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section
+
GenBank - GenBank entries at NCBI
  
−
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
+
RefSeq - RefSeq entry at NCBI
  
 +
UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot (reviewed) entry
  
−
The '''OTHER CROSSREFERENCES''' section contains accession numbers from the following databases:
+
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL (unreviewed) entry
  
 +
UniProtKB/GCRP - UniProt Knowledgebase, Gene-Centric Reference Proteome (GCRP) entry (the 'canonical' isoform representing the product(s) of each protein-coding gene)
  
−
EPD - Eukaryotic Promoter Database (Bucher)
+
==References==
  
−
GCR - The G protein-coupled receptor database
+
A list of publications that discuss the gene, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Gene Report.
−
 
 
−
InterPro - a database of protein families, domains and functional sites
 
  
−
MEROPS - Protease database
+
The icon the top left of the list of publications lists export/download options. 'Filter' allows a text search of the publications associated with the gene and there is a drop-down 'Sort by' option to order publications.
  
−
MIR - miRBase, microRNA data
+
Where available, a thumbnail image of the graphical abstract of the reference is shown to the right of the citation. Clicking on this shows the full size image in a pop-up window, which is itself hyperlinked to the relevant webpage on the journal's website.
  
−
MITODROME - The MitoDrome database
+
The default view of publications for protein-coding genes is the '''Representative Publications''' field. This aims to display papers (up to 100) that are most likely to contain the most information on the gene. These publications are identified and scored using an algorithm that assesses the amount and type of data within FlyBase attached to each gene, from each publication. The annotation data being assessed includes (in order of significance): the presence of the gene name/symbol in the title/abstract, the number of Gene Ontology annotations, the number of mutant alleles, the presence of antibody data and the presence of expression data.
−
 
 
−
NRL_3D - NRL_3D database
 
−
 
 
−
PDB - Protein Data Bank (Brookhaven)
 
−
 
 
−
Rfam - RNA families database of alignments and CMs
 
−
 
 
−
TransFac - The TRANSFAC database of transcription factors and their binding sites
 
−
 
 
−
 
 
−
The '''LINKOUTS''' section contains linkout identifiers from the following databases:
 
−
 
 
−
 
 
−
BDGP in situ Gene Expression Database - Patterns of gene expression in Drosophila embryogenesis
 
−
 
 
−
BioGRID - General Repository for Interaction Datasets
 
−
 
 
−
DEDB - Drosophila Exon Database
 
−
 
 
−
Drosophila PIMRider - The Drosophila Protein Interaction map
 
−
 
 
−
DRSC - Drosophila RNAi Screening Center
 
−
 
 
−
FLIGHT - Integrating Genomic and High-Throughput data
 
−
 
 
−
Flyatlas - the Drosophila adult expression atlas
 
−
 
 
−
FlyMine - An integrated database for Drosophila and Anopheles genomics
 
−
 
 
−
FlyView - A Drosophila Image Database
 
−
 
 
−
Genome RNAi, Heidelberg - a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells
 
−
 
 
−
Inparanoid - Eukaryotic Ortholog Groups
 
−
 
 
−
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
 
−
 
 
−
GEO - NCBI's Gene Expression Omnibus
 
−
 
 
−
Reactome - Curated Database of Biological Pathways
 
−
 
 
−
PANTHER - Protein Classification System
 
−
 
 
−
Yale Developmental Gene Expression
 
−
 
 
−
==Synonyms & Secondary IDs==
 
−
 
 
−
===Reported As===
 
−
 
 
−
{| class="wikitable" style="width: 100%;"
 
−
|-
 
−
|'''Symbol Synonym''' || style="width: 80%;" | A list of symbols that have been used in the literature, or by FlyBase, to describe the gene.
 
−
|-
 
−
|'''Name Synonym''' || A list of names that have been used in the literature, or by FlyBase, to describe the gene.
 
−
|}
 
−
 
 
−
===Secondary FlyBase IDs===
 
−
 
 
−
A list of Secondary FlyBase identifier numbers of the gene.
 
−
 
 
−
If a gene has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.
 
−
 
 
−
==References==
 
−
 
 
−
A list of publications that discuss the gene, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Gene Report.
 

Latest revision as of 21:09, 25 June 2024

Last Updated: 14th October 2022


The Gene Report provides information on individual genes. The report also contains summaries and links to individual reports relating to objects associated with the gene, such as mutant alleles of the gene (including both classical alleles and alleles carried within transgenic constructs), transcripts and proteins encoded by the gene and their expression pattern data, and transgenic constructs and insertions. A link to search for stocks carrying these objects is also provided.

A locus may have been mapped to the genome and have an annotation, or it may only have been identified genetically via its mutant phenotype. Both types of locus are given gene reports in FlyBase.

As well as including gene reports for genes derived from species within the family Drosophilidae, FlyBase also includes 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.

FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data.

This is a field-by-field guide to the information provided in the Gene Report.

General Information

Symbol The valid symbol that is used in FlyBase for the gene.

The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the gene symbol is used throughout FlyBase. For D.melanogaster genes, the species prefix is only displayed in the General Information section at the top of a Report.

Name The valid full name that is used in FlyBase for the gene.
Feature type A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the key type of the gene.

The single term in this field is computed by FlyBase from the full list of SO terms listed in the Sequence Ontology: Class of Gene section of the Gene Report.

See Computed Feature type of genes for a detailed description of how the term is selected.

Gene Model Status The status of the gene model, which represents the summation of the sequence level descriptions of the mature transcripts and, for protein coding genes, coding sequences and polypeptides encoded by an individual gene. Status is reported as follows:

Current The gene has a current gene model (indicated in the report by the presence of an annotation symbol and genomic sequence location).

Uncertain The gene has a current gene model, but supporting data are either inconclusive or ambiguous. Please see "Comments on Gene Model" section of the Gene Report for further explanation.

Incomplete FlyBase annotators have determined that this gene model is incomplete due to genomic assembly/sequencing gaps or unidentified translation start sites.

Withdrawn The gene had a gene model in a previous FlyBase release, but newer data do not support the existence of such a gene model.

Unannotated The gene doesn't have, and has never had, a gene model; the gene is inferred to exist from genetic data only, or, it does not map to the reference genome assembly.

Not Applicable (N/A) There is no FlyBase gene model (and thus no gene model status) for certain types of gene records: non-Drosophilid genes (e.g., Scer\GAL4, Avic\GFP); synthetic genes (e.g., Hsap\T:Hsap\MYC, Zzzz\T:Zzzz\FLAG); natural transposable element genes (e.g., Dmel\copia\GIP, Dmel\gypsy\pol); gene family records (e.g., Dmel\His2A).

Species The organism that the gene originates from, with the initial letter of the genus and the full species name listed.
Annotation symbol The current symbol for the annotation that represents the gene (if applicable).
FlyBase ID The Primary FlyBase identifier number of the gene, used to uniquely identify the gene in the database.

A gene may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Gene Report.

Stock availability A list of experimental lines relating to this gene that are available for order from public stock centers.
Enzyme Name (EC) Where relevant, the systematic name(s) for an enzyme together with its Enzyme Commission (EC) number(s). These data are derived from our Gene Ontology (GO) Molecular Function annotations by using the EC cross-references within the GO. Each EC number is linked to the corresponding page at the ExPASy ENZYME database.
Gene Summary A summary is shown at the top of every D. melanogaster gene report, with precedence given to the manually written Gene Snapshot. Where a Gene Snapshot is unavailable, a summary contributed by UniProtKB, Interactive Fly, Alliance of Genome Resources or the automated FlyBase gene summary is shown instead.
All Summaries Links to all the summaries available for this gene.
Also Known As Symbol synonyms that do not match the current gene symbol or annotation ID but have been used to refer to the gene in at least two papers. A maximum of ten case-insensitive synonyms are shown - when synonyms differ only by case, the version associated with most papers is reported.
Keys Links Links to the corresponding pages at other key bioinformatic resources, specifically the Alliance of Genome Resources, NCBI Gene, Ensembl, UniProtKB (canonical isoform from the gene-centric reference proteome (GCRP)) and RNAcentral, the latter two dependent on whether the gene is protein-coding or not. Full and explicit crossreferences for these and other resources are shown in the ‘External Crossreferences and Linkouts’ section.

Genomic Location

Cytogenetic Map A computed cytological location, based on the position on the genome to which the gene maps. This field is only filled in for genes with annotations.

See Computed cytological data for a detailed description of how this computed cytological location is calculated.

Sequence location The extent of the transcription unit on the genome, prefixed with the chromosome arm that the gene is located on. The strand to which the gene maps is indicated in square brackets after the sequence coordinates.

This field is only filled in for genes with annotations.

Recombination Map A computed genetic map position for the gene.
RefSeq locus The RefSeq locus ID for the chromosomal scaffold containing the gene, and the coordinates of the gene within that scaffold. Linked to the corresponding RefSeq entry.
Sequence There are options for downloading sequences associated with the gene. The drop-down menu allows the selection of the sequence of interest. The button beneath returns the sequence via the Sequence Downloader tool.

The following sequences can be downloaded:

Gene region

Extended Gene region

CDS

Introns

Exons

Transcripts

Translations

5' UTR

3' UTR

Genomic Maps A JBrowse thumbnail showing the location of the gene (highlighted in yellow) in the genome. Clicking on any of the genes visible in the thumbnail will take you to the corresponding gene report.


To the left of the JBrowse thumbnail, there are links to the JBrowse tool.

Other Genome Views Links to external genome browsers.

Foreign Gene Data

This section is only displayed in an individual Gene Report is for a "foreign gene", i.e. any non-drosophilid gene that has been introduced into Drosophila, for example via a transgenic construct. This section shows the species from which the gene is derived, the gene symbol, and where possible an accession number for the gene (either an identifier number from a human or model organism database, or a sequence accession number).

Function

GO Summary Ribbons GO Summary Ribbons are graphical summaries, designed to give an immediate overview of a gene product's properties and depth of characterization. They are derived from the Gene Ontology (GO) terms associated with the gene, divided into aspects of molecular function, biological process and cellular component. The GO annotations are grouped under high-level summary categories and are presented as colored cells in the row or 'ribbon' (see mapping table below for details). The depth of color of each cell indicates how many unique terms are grouped in a particular category. The unique terms that group under a particular cell can be seen by mousing-over the cell. Some terms may group under more than one cell because the GO allows multiple ancestry.
Gene Ontology (GO) Annotations Gene Ontology (GO) controlled vocabulary (CV) terms assigned to genes based on evidence in external publications and internal analysis. Note that terms are assigned to genes but apply to the product of that gene. The number in parentheses shows the total number of different terms assigned to a gene.

Annotations are divided into three subsections:

Molecular Function

Biological Process

Cellular Component

Within each subsection the terms are divided into 'Terms Based on Experimental Evidence' and 'Terms Based on Predictions or Assertions'.

GO term: Clicking on the term in the CV term column will take you to the relevant GO CV Term Report, which includes a definition of the GO term.

Gene product to term relations: GO CV terms are preceded by a gene product to term relation which imparts a relational meaning between the term and the gene product.

NOT: The qualifier NOT is used to make an explicit note that the gene product is not associated with the GO term.

Evidence: The type of evidence used to support the GO term is indicated in the evidence column. The evidence code documentation contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology Guide to GO Evidence Codes. Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the GO.xrf_abbs file. The evidence code documentation explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.

More information about how GO terms are assigned can be found under the Classification of Gene Products using Gene Ontology (GO) terms. The current release of GO data for all FlyBase genes can be found in the gene_association.fb file. The latest version of this data is available for download here from the Gene Ontology consortium site. Details about the file format and comments on version differences can be found in the documentation on the Classification of Gene Products using Gene Ontology (GO) terms

Gene Group (FlyBase) Lists any FlyBase Gene Groups the gene is a member of, with a link to the Gene Group Report.
Pathway (FlyBase) Lists any FlyBase Pathways the gene is a member of, with a link to the Pathway Report.
Protein Family (UniProt) Lists any UniProt Protein Families shown in their 'Sequence similarities' section, with the evidence code and a link to corresponding UniProt page.
Protein Signatures (InterPro) Lists InterPro protein domains or motifs found in the protein encoded by the gene with link to the corresponding InterPro page.
Catalytic Activity (EC/Rhea) Where relevant, the reaction(s) catalyzed by an enzyme together with their Enzyme Commission (EC) number(s) and RHEA ID(s). These data are derived from our Gene Ontology (GO) Molecular Function annotations by using the EC/Rhea cross-references within the GO. EC numbers are linked to the corresponding page at the ExPASy ENZYME database, and RHEA IDs are linked to the corresponding page at the Rhea database. Clicking on an image of reactant/product in the Rhea graphic links to the corresponding page at the ChEBI database.


GO Summary Ribbon mapping tables:


molecular function

slimming path relations: is_a, part_of

Tile Name GO term(s) GO ID(s)
enzyme catalytic activity GO:0003824
regulator molecular function regulator GO:0098772
receptor signaling receptor activity GO:0038023
receptor binding signaling receptor binding GO:0005102
transporter transporter activity GO:0005215
structural molecule structural molecule activity GO:0005198
cytoskeleton binding cytoskeletal protein binding GO:0008092
DNA binding DNA binding GO:0003677
RNA binding RNA binding GO:0003723
transcription factor transcription regulator activity GO:0140110
small molecule binding small molecule binding GO:0036094
metal ion binding metal ion binding GO:0046872
lipid binding lipid binding GO:0008289
carbohydrate binding carbohydrate binding GO:0030246
other molecular_function Any term that does not map to the above Any ID that does not map to the above


biological process

slimming path relations: is_a, part_of, regulates


Tile Name GO term(s) GO ID(s)
cell cycle/proliferation cell cycle,cell proliferation GO:0008283, GO:0007049
cellular organization/biogenesis cellular component organization or biogenesis GO:0071840
cellular transport/localization macromolecule localization, establishment of localization GO:0051234, GO:0033036
development developmental process GO:0032502
reproduction reproduction GO:0000003
immune system immune system process GO:0002376
nervous system process nervous system process GO:0050877
behavior behavior GO:0007610
response to stimulus response to stimulus GO:0050896
signaling signaling GO:0023052
gene expression gene expression GO:0010467
protein metabolism protein metabolic process GO:0019538
DNA metabolism DNA metabolic process GO:0006259
small molecule metabolism small molecule metabolic process GO:0044281
other biological_process Any term that does not map to the above Any ID that does not map to the above


cellular component

slimming path relations: is_a, part_of

Tile Name GO term(s) GO ID(s)
extracellular extracellular region GO:0005576
cytosol cytosol GO:0005829
cytoskeleton cytoskeleton GO:0005856
mitochondrion mitochondrion GO:0005739
nucleus nucleus GO:0005634
chromosome chromosome GO:0005694
membrane membrane GO:0016020
cell periphery cell periphery GO:0071944
cell projection cell projection GO:0042995
endomembrane system vacuole, endomembrane system GO:0005773, GO:0012505
synapse synapse GO:0045202
macromolecular complex protein-containing complex GO:0032991
other cellular_component Any term that does not map to the above Any ID that does not map to the above

Summaries

Gene Snapshot A short summary designed to provide a quick overview of the function of the gene's products. It is based on key points solicited from expert researchers, and revised by FlyBase curators. The review date is stated, and cases that are in progress or are deemed to have insufficient data to summarize are stated as such.
Automated Description (Alliance of Genome Resources) Automated, standardised descriptions for D. melanogaster and human genes imported from The Alliance of Genome Resources. These descriptions currently summarize data on gene function, disease associations and orthology to human genes.
Automatically Generated Summary (FlyBase ) Generated automatically by FlyBase from information in the gene report and related allele reports. For more information about each statement in the summary see the relevant section in the gene gene/allele report.
Pathway (FlyBase) Manually written summary for the FlyBase Pathway Group(s) of which the gene is a member. The Pathway Group name is hyperlinked to the corresponding Pathway Group Report.
Gene Group (FlyBase) Manually written summary for the FlyBase Gene Group(s) of which the gene is a member. The Gene Group name is hyperlinked to the corresponding Gene Group Report.
Protein Function (UniProtKB) Shows the summary shown in the UniProt 'Function' section, with a hyperlink to corresponding UniProt page.
Phenotypic Description (Red Book; Lindsley and Zimm 1992) Phenotypic descriptions of mutants of this gene from the Red Book (Lindsley and Zimm 1992). Gene/Allele symbols may differ from current usage.
Summary (Interactive Fly) Shows a summary of the gene from Interactive Fly. Links to the summary on the FlyBase wiki and to the gene page in Interactive Fly.

Gene Model & Products

Number of Transcripts

The number of transcripts annotated for the gene are given.

Number of Unique polypeptides

The number of unique polypeptides annotated for the gene are given.

JBrowse Graphic

A JBrowse graphic showing the gene model. The grene's transcripts, CDS and any transgene insertion sites in the region are shown. For a more detailed view showing more features, a link to open JBrowse in a separate window is provided above the graphic.

Protein Domains (via Pfam)

An image displaying protein domains predicted by Pfam are displayed on the longest polypeptide isoform. Mousing over the domains displays a window showing the full domain name and the amino acid position in the polypeptide.

The corresponding InterPro data is shown in a table below.

Protein Domains (via SMART)

An image displaying protein domains predicted by SMART are displayed on the longest polypeptide isoform. Mousing over the domains displays a window showing the full domain name and the amino acid position in the polypeptide.

The corresponding InterPro data is shown in a table below.

Structure

As appropriate, this section shows a prediction of the 3D protein structure or a 2D RNA structure, where available.

Protein 3D structure (Predicted by AlphaFold)

For protein-coding genes, this section displays the 3D protein structure predicted by AlphaFold. Only the UniProt 'canonical isoform' is shown for a given protein, and structures are not available for all proteins - see the AlphaFold FAQ for more details. The UniProt accession of the protein is given in the section header and links to the corresponding AlphaFold webpage. The image can be zoomed and rotated using a mouse/trackpad. Several display aspects can be changed and customised using the buttons within the image.

RNA 2D structure (Predicted by RNAcentral)

For relevant non-coding RNA (ncRNA) genes, this section displays the 2D structure for ncRNAs predicted by R2DT and as shown within RNAcentral. Structured ncRNAs include tRNAs, rRNAs, snRNAs, snoRNAs and the RNA components of RNase P, RNase MRP and SRP. The RNAcentral identifier is given in the section header and links to the corresponding RNAcentral webpage. The image can be zoomed and repositioned using a mouse/trackpad. Several display aspects can be changed and customised using the buttons within and above the image - see the RNAcentral documentation for more details.

Comments on Gene Model

Comments regarding the annotation of the gene, including whether the gene model contains any unconventional features.

Sequence Ontology: Class of Gene

A list of controlled vocabulary terms from the Sequence Ontology (SO), which describe the class of the gene. Aspects of the gene class which are described by the SO terms include (but are not limited to):

- the type of molecule (e.g. protein, tRNA, rRNA) encoded by the gene.

- where the gene is encoded (e.g. nucleus, mitochondrion).

Transcript Data

Annotated Transcripts

A table listing the annotated transcripts of the gene, their FlyBase identifier number, length in nucleotides and length in amino acid residues of the associated coding sequence (CDS). Clicking on a transcript symbol will take you to the relevant Transcript Report.

Additional Transcript Data & Comments

Reported transcript sizes (kB) A list of transcript sizes that have been reported in the literature along with the associated reference.
Comments Miscellaneous free text comments related to reported transcripts along with the associated reference.

External Data

A list of accession numbers from external databases that are relevant to the transcripts of the gene. The accession numbers are FlyBase curated links.

Accession numbers from the following databases are currently displayed in this section:


MIR - miRBase, microRNA data

Rfam - RNA families database of alignments and CMs

These links are also displayed together with all other external data links for the gene in the External Crossreferences and Linkouts section of the Gene Report.

Polypeptide Data

Annotated Polypeptides

A table listing the annotated polypeptides of the gene, their FlyBase identifier number, predicted molecular weight (kD), length in amino acid residues, theoretical pI, and GenBank protein accession numbers. Clicking on a polypeptide symbol will take you to the relevant Polypeptide Report.

Additional Polypeptide Data & Comments

Reported protein sizes (kB) A list of protein sizes that have been reported in the literature along with the associated reference.
Comments Miscellaneous free text comments related to reported proteins along with the associated reference.

External Data

A list of links to external databases that are relevant to the polypeptides encoded by the gene. These links are also displayed together with all other external data links for the gene in the External Crossrefences and Linkouts section of the Gene Report.

Sequences Consistent with the Gene Model

A table of sequence accession numbers that support the gene model. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived. Sequences associated with genes that do not yet have an annotation are also listed in this section.

The table contains accession numbers from the following databases:


DDBJ/EMBL/GenBank - nucleic acid accession number and associated protein ID number (if applicable).

UniProtKB/Swiss-Prot - protein accession number.

UniProtKB/TrEMBL - protein accession number.


These accessions are both FlyBase curated links and associations made by automated assessment of aligned cDNA and EST nucleotide sequences.

Mapped Features

A table listing features associated with the gene, additional to the basic transcript and polypeptide structure, that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains the feature's name as well as its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.

External Data

A list of links to external databases that are relevant to the gene model as a whole, but not specifically to individual gene products.

These links are also displayed together with all other external data links for the gene in the External Crossreferences and Linkouts section of the Gene Report.

Expression Data

Expression Summary Ribbons

The expression ribbons provide a graphical overview of expression data from three sources.

1. adult cell types - Fly Cell Atlas scRNA-seq

Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene with dark red indicating the highest levels of expression. Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.


Ribbon - FBbt mapping table:

Tile Name FBbt term FBbt ID
neuron neuron FBbt:00005106
interneuron interneuron FBbt:00005125
motor neuron motor neuron FBbt:00005123
sensory neuron sensory neuron FBbt:00005124
sensory organ cell sensory organ cell FBbt:00005163
glial cell glial cell FBbt:00005144
muscle cell muscle cell FBbt:00005074
tendon cell tendon cell FBbt:00005090
epithelial cell epithelial cell FBbt:00000124
epidermal cell epidermal cell FBbt:00007325
Malpighian tubule cell specialized Malpighian tubule cell FBbt:00005794
nephrocyte nephrocyte FBbt:00047125
tracheocyte tracheocyte FBbt:00005038
fat cell fat cell FBbt:00046052
hemocyte hemocyte FBbt:00005063
oenocyte oenocyte FBbt:00004995
somatic precursor cell somatic precursor cell FBbt:00007008
somatic cell of ovariole somatic cell of ovariole FBbt:00006030
somatic cell of testis somatic cell of testis FBbt:00006031
female germline cell female germline cell FBbt:00057012
male germline cell male germline cell FBbt:00057011
male semen-secreting cell semen-secreting cell of the male reproductive system FBbt:00058293
other cell type Any term that does not map to the above Any ID that does not map to the above

2. anatomy - manually curated

Transcript and polypeptide expression data manually curated by FlyBase from individual publications is presented in a simple yes/no ribbon, in which the presence of curated data is marked by a colored tile. A colorless tile represents absence of manually curated data and can not be used to deduce the absence of expression. The ribbon is generated by using high-level summary categories to group expression curated using the Fly Anatomy Ontology (FBbt).(See table below for mapping.) The complete data used to generate this ribbon can be viewed in the Transcript and Polypeptide sections below the ribbon section.

Note that expression data from reporters is not used to populate the anatomy ribbon.


Ribbon - FBbt mapping table:

Tile Name FBbt term(s) FBbt ID(s)
egg/oocyte egg, oocyte FBbt:00000034, FBbt:00004886
stem cell stem cell FBbt:00007014
imaginal tissue imaginal tissue FBbt:00047552
anlage/primordium anlage, primordium FBbt:00005426, FBbt:00005495
sensory system sensory system, embryonic sensory system FBbt:00007692, FBbt:00005827
nervous system nervous system, presumptive embryonic/larval nervous system FBbt:00005093, FBbt:00001055
circulatory system circulatory system, presumptive embryonic/larval circulatory system FBbt:00005057, FBbt:00005676
tracheal system tracheal system, presumptive embryonic/larval tracheal system FBbt:00005024, FBbt:00005569
digestive system digestive system, presumptive embryonic/larval digestive system FBbt:00005055, FBbt:00000438
adipose system adipose system, presumptive embryonic/larval adipose system FBbt:00005065, FBbt:00005708
endocrine system endocrine system, presumptive embryonic/larval endocrine system FBbt:00005068, FBbt:00005712
excretory system excretory system FBbt:00005056
reproductive system reproductive system FBbt:00004857
integumentary system integumentary system, presumptive embryonic/larval integumentary system FBbt:00004969, FBbt:00005392
muscle system muscle system, presumptive embryonic/larval muscle system FBbt:00005069, FBbt:00005647
other anatomical entity Any term that does not map to the above Any ID that does not map to the above

3. stages - modENCODE RNA-seq

High-throughput stage specific RNA-seq expression data is presented as a heat map, where a white tile represents no expression detected and the gradient range, from lowest to highest expression bin, is colored from yellow/green to red. This ribbon is a compressed version of the data from the modENCODE RNAseq project. Complete data can be viewed in the modENCODE Development RNA-Seq section under High-Throughput Expression.

Testis-specificity index

The testis-specificity index was calculated by Vedelek et al., 2018 from modENCODE tissue expression data. The scores indicate the degree of testis bias in expression and range from -2.52 (underrepresented) to 5.2 (very high testis bias).

Transcript Expression

A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by location of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages, anatomical parts and subcellular localization are described using controlled vocabulary terms.

The table is subdivided by the assay, when appropriate.

Additional Descriptive Data

Free-text curated descriptions of expression patterns, sorted by year of reference.

Marker for

An anatomical structure or cellular component where the expression of a gene has been used as a marker for a particular tissue or developmental state.

Subcellular Localization

A table of Gene Ontology (GO) cellular component terms that describe the subcellular location of the transcript(s) of this gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided.

Polypeptide Expression

A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by location of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages, anatomical parts and subcellular localization are described using controlled vocabulary terms.

The table is subdivided by the assay used, when appropriate.

Additional Descriptive Data

Free-text curated descriptions of expression patterns, sorted by reference.

Marker for

An anatomical structure or cellular component where the expression of a gene has been used as a marker for a particular tissue or developmental state.

Subcellular Localization

A list of Gene Ontology (GO) cellular component terms that describe the subcellular location of the polypeptide(s) of this gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided.

Expression Deduced from Reporters

Reporters are listed as a series of tables. In the subsection header, the reporter symbol is linked to the relevant report. A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by location of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages, anatomical parts and subcellular localization are described using controlled vocabulary terms.

High-Throughput Expression Data

Associated Tools: Links to associated tools that enable visualization and searching of High-Throughput Expression Data
- JBrowse: view the gene's RNA-Seq signal across genomic regions.
- RNA-seq: view expression profiles for each of the gene's exons across development or various tissues.

Bulk Downloads: Download file of RNA-Seq RPK values for all genes.

Reference: Reference for high-throughput expression data set.

FlyAtlas Anatomy Microarray

Microarray expression values are provided by FlyAtlas and genes are sorted into one of five gene expression level bins by FlyBase (from "No expression" to "Very high expression"). See the FlyAtlas-RNA.adult and FlyAtlas-RNA.larva dataset reports for details.

modENCODE RNA-Seq

RNA-Seq expression values are calculated by FlyBase from coverage data (provided to us by the modENCODE project), as described by Gelbart and Emmert, 2013; genes are sorted into one of eight gene expression level bins (from "No/Extremely low expression" to "Extremely high expression"). Expression values are presented as user-configurable histograms/heatmaps, color-coded by expression level bin. Expression values can be downloaded as a tab-separated values (.tsv) file. Links to the relevant dataset reports are at the top left of each section.


modENCODE Anatomy RNA-Seq - see the modENCODE_mRNA-Seq_U dataset report for details.

modENCODE Development RNA-Seq - see the modENCODE_mRNA-Seq_tissues dataset report for details.

modENCODE Cell Lines RNA-Seq - see the modENCODE_mRNA-Seq_cell.B dataset report for details.

modENCODE Treatments RNA-Seq - see the modENCODE_mRNA-Seq_treatments dataset report for details.

NIH Anatomical Expression RNA-Seq' - expression levels for D. pseudoobscura genes from modENCODE RNA-Seq datasets: NIH_mRNA_Dpse_gonads_carcasses, NIH-Dpse_1_adult_heads and NIH_mRNA_Dpse_2_adults.

Developmental Proteome

Normalized, label-free quantitative (LFQ) protein expression was obtained from Casas-Vila et al., 2017 for about 8,000 protein coding genes. Expression values are sorted into one of seven expression level bins (from "at/below limit of detection" to "very high expression"). Expression values are presented as user-configurable histograms, color-coded by expression level bin. Expression values can be downloaded as a tab-separated values (.tsv) file. Links to the relevant dataset reports are at the top left of each section.

Developmental Proteome: Embryogenesis - see the Casas-Vila_proteome_embryogenesis dataset report for details.

Developmental Proteome: Life Cycle - see the Casas-Vila_proteome_life_cycle dataset report for details.

External Data and Images

This section includes:

Linkouts to external resources.

Expression pattern images.

A link to the FlyBase wiki image resources page.

Alleles, Insertions and Transgenic Constructs

A series of tables containing classical and insertion alleles, transgenic constructs and aberrations relevant to the gene.

Documentation In Progress The tables in this section have recently been updated to give more flexibility when searching the genetic reagents that are available for your favorite gene. See this FlyBase Commentary for more information.

Classical and Insertion Alleles

The number in parentheses in the section header shows the total number of classical and insertion alleles that exist in FlyBase for this gene.

A table listing all the classical and insertion alleles of the gene.


Other relevant insertions

A table showing other relevant insertions that affect the gene, either because the insertion maps within the transcription unit, and/or it has been shown to reflect the expression of the gene.


Transgenic Constructs

The number in parentheses in the section header shows the total number of transgenic constructs that exist in FlyBase containing/affecting coding region for this gene.

Transgenic constructs containing/affecting coding region of gene

A table listing all the transgenic constructs containing/affecting the coding region of the gene.


Transgenic constructs containing regulatory region of gene

A table showing transgenic constructs containing the regulatory region of the gene.


Aberrations (Deficiencies and Duplications)

The number in parentheses in the section header show the total number of deletions and duplications

Gene disrupted in A list of aberrations that have been reported to completely delete/disrupt the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Gene partially disrupted in A list of aberrations that have been reported to partially disrupt the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Gene not Disrupted in A list of aberrations that have been reported not to disrupt the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Gene duplicated in A list of aberrations that have been reported to completely duplicate the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Gene partially duplicated in A list of aberrations that have been reported to partially duplicate the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Gene not duplicated in A list of aberrations that have been reported not to duplicate the gene, determined by either complementation or molecular analysis.

Clicking on an aberration symbol will take you to the relevant Aberration Report.

This field is only displayed in an individual Gene Report if it contains data.

Variants

Variant Molecular Consequences Variants data from FlyBase are run through the Ensembl VEP (Variant Effect Predictor) pipeline, and the results are displayed in a scrolling table. The VEP algorithm considers the genomic location, mutation type, and nucleotide change of a variant to calculate the molecular consequence on all of the overlapping transcripts affected by the variant. In addition to reporting the molecular change to the transcripts and encoded CDS, it assigns a Sequence Ontology (SO)-based consequence term to each variant/transcript combination.

The table displays, for each variant, all genes that are potentially affected by that variant, any alleles of those genes associated with the variant, and the predicted consequences to all affected transcripts. The gene that is the subject of the report is highlighted in the table.

This is the result of a collaboration between FlyBase, Alliance of Genome Resources and Ensembl.

Alleles Representing Disease-Implicated Variants A table showing mutants or transgenic alleles that have been used as models for a human disease. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model.

The results are shown in an interactive table with columns for allele, human variant designation, human variant synonyms, external links, human disease model, the originating reference, the number of references associated with the allele, and comments.

The tables have many features to optimize usability, including pagination for very large lists, row filtering by column (click on the column heading), row sorting by column (insert search term in the Filer... box), the ability to hide/show individual columns (access from button at upper right corner of table), column reordering (click and drag the column header), and the ability to export to a Hitlist, CSV, or Excel (button at upper left corner of table).

Phenotypes

A table containing a summary of the phenotypes of alleles of the gene. The table lists controlled vocabulary terms describing the phenotype, together with the allele(s) of the gene which have been reported to show this phenotype.

To see the detail of the phenotype (including publications where the phenotype has been reported and additional free text comments), click on the allele symbol to go to the relevant Allele Report and look at the Phenotypic Data section.

Clicking on the controlled vocabulary term will take you to the relevant CV Term Report, which includes a definition of the term (where available).

Section Description
Lethality A list of reported lethal/viable phenotypes.
Sterility A list of reported sterile/fertile phenotypes.
Other Phenotypes A list of other reported phenotypic classes.
Phenotype manifest in A list of the parts of the animal reported to be affected in the mutant alleles.

Orthologs

The orthologs section presents orthology calls between D. melanogaster and other species provided by DRSC Integrative Ortholog Prediction Tool (DIOPT) for human and model organism species and OrthoDB for other species. The complete set of orthology calls for DIOPT can be downloaded using the buttons at the top of the section and for the subsections via the download thumbnails in the subsection header bar.

Human Orthologs (via DIOPT)

This section presents orthology calls between D. melanogaster and human, as provided by the DRSC Integrative Ortholog Prediction Tool (DIOPT). The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is here.)

The columns are:

  • Species\Gene Symbol: the official human gene symbol and name, as used at (and linked to) the HGNC prefixed with the Hsap 4-letter species abbreviation used in FlyBase. The NBCI thumbnail links to the gene report page at NCBI.
  • Best Score: either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
  • Best Rev Score: either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
  • Source: check-boxes indicating which individual ortholog prediction tools support a given orthologous gene-pair relationship
  • 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")
  • Alignment: link to an alignment between the given orthologous gene-pairs on the DIOPT site
  • Complementation?: Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been show to functionally complement the Dmel gene
  • Transgene?: Where applicable, a link in the form of a Drosophila icon to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila

Model Organism Orthologs (via DIOPT)

This section presents orthology calls between D. melanogaster and other model organisms, as provided by the DRSC Integrative Ortholog Prediction Tool (DIOPT). The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is here.)

The list of ortholog predictions is arranged by species, in order of increasing phylogenetic distance relative to human.

The columns are:

  • Species\Gene Symbol: official gene symbol, as used in (and linked to) the relevant model organism database, prefixed with the 4-letter species abbreviation used in FlyBase

The NBCI thumbnail links to the gene report page at NCBI.

  • 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")
  • Best Score: either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
  • Best Rev Score: either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
  • Source: check-boxes indicating which individual ortholog prediction tools support a given orthologous gene-pair relationship
  • Alignment: link to an alignment between the given orthologous gene-pairs on the DIOPT site
  • Complementation?: Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been shown to functionally complement the D. melanogaster gene
  • Transgene?: Where applicable, a link in the form of a Drosophila icon to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila

Other Organism Orthologs (via OrthoDB)

This section presents OrthoDB-derived orthology calls between D. melanogaster and other metazoa not included in the DIOPT orthology set, including other Drosophila species, dipterans, insects and arthropods. These data are retrieved directly from OrthoDB via API calls and therefore reflect the current OrthoDB version (which can be checked by clicking on the 'OrthoDB' link at the top of the section).

The columns are:

  • Organism: the latin species designation
  • Common Name: the common species name (when available)
  • Gene ID: symbol/ID of the orthologous gene, linked to the gene report at OrthoDB
  • OrthoDB description: name/description of the orthologous gene

Paralogs

The paralogs section presents paralogy calls within D. melanogaster as provided by DRSC Integrative Ortholog Prediction Tool (DIOPT). The DIOPT approach integrates paralog predictions from multiple tools, thereby giving an overview of potential paralogs derived from different algorithms. (Further documentation is here.)

The complete set of paralogy calls can be downloaded using the button at the top of the section.

The columns on the main table are:

  • Gene Symbol: the FlyBase gene symbol. The NBCI thumbnail links to the gene report page at NCBI.
  • Score: the number of tools that support a given paralogous gene-pair relationship compared to the total number of tools that compute paralogy relationships (expressed as "X of Y")
  • Source: check-boxes indicating which individual prediction tools support a given gene-pair relationship
  • Alignment: link to an alignment between the given gene-pairs on the DIOPT site

Human Disease Associations

FlyBase Human Disease Model Reports

Links to Human Disease Model Reports associated with this gene.


Disease Model Summary Ribbon

This ribbon summarizes Disease Ontology annotations for disease models in FlyBase, as given in the "Models Based on Experimental Evidence" and "Potential Models Based on Orthology" subsections below. (Modifier and negative annotations are excluded.) The ribbon is broken into broad categories of infection, anatomical entity, proliferation and other diseases, and is analogous to the equivalent ribbon used at the Alliance of Genome Resources.

Disease Ontology (DO) Annotations

Human Disease model data curated using disease terms from the Disease Ontology.

Models Based on Experimental Evidence 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.

The table consists of four columns:

Allele - The alleles of the gene that is being used as a model.

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 Disease Ontology).

Evidence - CEA (combinatorial experimental and author inference evidence used in manual assertion; ECO:0007013) is used when an annotation is made based on experimental evidence AND the disease term used agrees with that stated by the authors. This is the most commonly used evidence code. CEC (combinatorial experimental and curator inference evidence used in manual assertion; ECO:0007014) is used when an annotation is made based on experimental evidence BUT the disease term used has been determined by a curator rather than based on a statement by the authors of the paper. Use of this evidence code is relatively rare, restricted to cases where (i) the disease stated by the authors is relatively general (e.g. “amyotrophic lateral sclerosis”), but the curator can provide a more specific subtype (e.g. “amyotrophic lateral sclerosis type 6”) based on the given human gene/variant and its known relationship to a specific disease (e.g. in OMIM); or (ii) the authors have made a mistake in the given gene-to-disease relationship. If the given allele only models the disease in combination with another allele, the word 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.

References - lists the reference(s) that describe the model.

This information is also shown on the individual allele reports.

The information displayed in this table can be downloaded using the 'Models Data' button at the top of the section.

Potential Models Based on Orthology A table showing any disease(s) that are associated with the human ortholog of the given D. melanogaster gene.

The table consists of four columns:

Human Ortholog - the human gene orthologous to the given D. melanogaster gene

Disease - the name of the disease (from the Disease Ontology) associated with that human gene, as annotated in OMIM

Evidence - this is always 'inferred from electronic annotation'

References - lists the reference (FBrf0241599) describing the logic of this orthology-based algorithm.

Modifiers Based on Experimental Evidence A table showing interactions of this allele with other disease-causing allele(s)

The table consists of four columns:

Allele - The alleles of the gene that is being used as a model.

Disease - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the Disease Ontology). This column also indicates if the allele is not modifying a disease (prefixed with DOES NOT).

Interaction - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages.

References - lists the reference(s) that describes the model.

This information is also shown on the individual allele reports.

Comments on Models/Modifiers Based on Experimental Evidence Curated comments that highlight certain features of a model, for example, when particular aspects of a disease phenotype are modeled while others are not. These comments are used sparingly to avoid duplication with phenotype information.

This information is also shown on the individual allele reports.

The information displayed in this table can be downloaded using the 'Interactions Data' button at the top of the section.

Human Orthologs (via DIOPT) and Disease Associations

Orthology calls between D. melanogaster and human, as provided by the DRSC Integrative Ortholog Prediction Tool (DIOPT), together with links to relevant gene and phenotype reports at the Online Mendelian Inheritance in Man (OMIM) database. The DIOPT approach integrates ortholog predictions from multiple tools, thereby giving an overview of potential orthologs derived from different algorithms. (Further documentation is here.)

Only predicted orthologs with a score of equal or greater than 3 (at least three prediction tools support this prediction) are shown.

The columns are:

  • Gene Name: the official human gene symbol and name, as used at (and linked to) the HGNC
  • 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")
  • OMIM: the OMIM number for this human gene, linked to the corresponding OMIM gene report
  • OMIM Phenotype: any phenotypes associated with the human gene, as reported in OMIM, and linked to the corresponding OMIM phenotype report
  • DO Term: The Disease Ontology term equivalent to the given OMIM term, as determined by the OMIM cross-references within the DO.
  • Complementation: Where applicable, a link in the form of a yin-yang symbol to data indicating that an orthologous gene has been show to functionally complement the D. melanogaster gene
  • Transgene in Fly: Where applicable, a link to a FlyBase Gene Report for the human gene, indicating that it has been expressed transgenically in Drosophila

Functional Complementation Data

This section 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 table shows 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.

The columns are:

  • Dmel gene: current FlyBase symbol of Dmel gene
  • Ortholog showing functional complementation: 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.
  • Supporting References: list of publications that reported the suppression of a mutant phenotype of the Dmel gene by a transgenic construct/mutant allele of the non-Dmel ortholog.

Interactions

Summary of Physical Interactions

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.

esyN Network Diagram A graphical representation of FlyBase-curated physical interactions. Linkouts to the esyN tool allow users to edit the network display by adding/deleting additional factors and genetic or physical interactions to the diagram.

“Interactions Browser” To see a graphical representation of physical interactions involving this gene click the Interactions Browser button.


RNA-RNA A table containing a summary of "RNA-RNA" physical interactions between the RNA products of two genes. The table lists each pairwise RNA-RNA interaction on a separate line of the table. The two interacting genes are indicated in the first column. Each interaction is represented as a group of reported interaction instances. All assays used in support of the interaction are listed in column 2. All references reporting the pairwise interaction are listed in column 3. Clicking on a 'Interacting group' symbol will take you to the relevant Interaction Report. Clicking on a reference will take you to the relevant Reference Report.


RNA-protein This table reports physical interactions between the protein of one gene and the RNA of another gene. The table lists each pairwise RNA-protein interaction on a separate line of the table. The two interacting genes are indicated in the first column. Each interaction is represented as a group of reported interaction instances. All assays used in support of the interaction are listed in column 2. All references reporting the pairwise interaction are listed in column 3. Clicking on a 'Interacting group' symbol will take you to the relevant Interaction Report. Clicking on a reference will take you to the relevant Reference Report.


protein-protein A table containing a summary of "protein-protein" physical interactions between the protein products of two genes. The table lists each pairwise protein-protein interaction on a separate line of the table. The two interacting genes are indicated in the first column. Each interaction is represented as a group of reported interaction instances. All assays used in support of the interaction are listed in column 2. All references reporting the pairwise interaction are listed in column 3. Clicking on a 'Interacting group' symbol will take you to the relevant Interaction Report. Clicking on a reference will take you to the relevant Reference Report.

Summary of Genetic Interactions

Information regarding curated genetic interactions for the gene. To see the full details of the genetic interactions (including the alleles used and the phenotypes seen), see the Alleles and Phenotypes section.

esyN Network Diagram A graphical representation of FlyBase-curated genetic interactions. Linkouts to the esyN tool allow users to edit the network display by adding/deleting additional factors and genetic or physical interactions to the diagram.

Interactions browser - To see a graphical representation of genetic interactions involving this gene click the Interactions Browser button.

A table containing a summary of genetic interactions between this and other genes. The table lists other gene that this gene has been shown to interact with genetically, as well as the type of interaction (suppressible, enhanceable) and the reference(s) in which the interaction is described.

Clicking on a gene symbol will take you to the relevant Gene Report for the interacting gene.

Clicking on a reference will take you to the relevant Reference Report.

Pathways

Signaling Pathways (FlyBase)

Where relevant, this section gives a link to, and description of, any signaling pathway in which the given gene (product) is involved, as curated by FlyBase. (A list of currently curated pathways is here.)

Metabolic Pathways

This section shows link-outs to several different metabolic pathway resources(including KEGG Pathway, Reactome and BioCyc) that include the gene (product) within the given metabolic pathway or process.

External Data

This section shows link-outs to several different pathway resources (including KEGG Pathway, Reactome and SignaLink) that include the gene (product) within the given signaling pathway or other process.

Genomic Location and Detailed Mapping Data

Chromosome (arm) The chromosome arm that the gene is located on. This field is only filled in for genes with annotations.
Cytogenetic Map A computed cytological location, based on the position on the genome to which the gene maps. This field is only filled in for genes with annotations.

See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated.

Recombination map A computed genetic map position for the gene, derived from the full list of terms listed in the Experimentally Determined Recombination Data subsection.

The genetic map position is given as chromosome number-map position, or simply chromosome number, if the gene has not been mapped within the chromosome.

Sequence location The extent of the transcription unit on the genome, prefixed with the chromosome arm that the gene is located on. The strand to which the gene maps is indicated in square brackets after the sequence coordinates.

This field is only filled in for genes with annotations.

FlyBase Computed Cytological Location

An inferred cytological location, based on the position on the genome to which the gene maps, or on polytene localization, recombination, complementation or molecular information for the gene. The evidence that was used to derive the inferred location is also given.

See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated.

Experimentally Determined Cytological Location

A table of cytological locations that have been reported for the gene in the literature. The table also contains additional notes on the reported location, such as a comment that the cytological location is inferred from the location of a transposable element insertion causing an allele of a gene.

Experimentally Determined Recombination Data

A table of genetic map data that have been reported for the gene in the literature. The table contains reported genetic map positions, given as chromosome number-map position, or simply chromosome number, if the gene has not been mapped within the chromosome.

The table also lists other genes to which the gene has been mapped to the left of or right of, and additional notes on the reported location.

If a gene has been mapped cytogenetically but not genetically, an estimated genetic position may be given in square brackets, inferred from a standard Map Conversion Table.

Stocks and Reagents

Stocks

A list of the stocks from the public stocks centers that contain this gene; genotypes may be provided. The number of stocks is indicated in parentheses. If there are a large number of stocks, the list may be truncated. Click on the 'More stocks available' button to show all in a FlyBase HitList. For participating stock centers, clicking on the stock number will take you to the appropriate stock report.

Genomic Clones

A list of genomic clones that are associated with this gene. The number of genomic clones is indicated in parentheses. Clicking on the 'List GenBank IDs' button generates a table of genomic clones related to the gene with links to GenBank records.

Note: FlyBase no longer curates genomic clone accessions so this list may not be complete.

cDNA Clones

This section lists cDNA clones that have been associated with this gene. The number of cDNA clones is indicated in parentheses. It is subdivided to distinguish fully sequenced clones from those which have only been partially characterized. Clones that are part of the BDGP DGC collection are listed separately from the other clones.

These associations are primarily automated and at this time include clones containing inserts that support the gene model as well as clones containing inserts that overlap the gene model but do not support any of the currently annotated transcripts. Efforts have been made to eliminate from this list clones that overlap the gene model but support another gene model in the same genomic region (i.e. a gene nested within an intron of another gene). In addition, clones containing sequences that overlap transposable elements have been excluded from this list.

We plan to subdivide clones into those that completely support a gene model and those that overlap but do not support an annotation in a future iteration of the report but at this time care should be taken to assess the sequences linked to the clone before using a clone as a reagent.

RNAi & Array Information

Linkouts to RNAi and array resources. Clicking on the linkout identifier will take you to the appropriate clone report entry in the external database from which they are derived.

Resources currently listed include

DRSC

GenomeRNAi

Antibody Information

A list of publications in which the generation of antibodies against the subject polypeptide has been reported. Each entry is categorized as "polyclonal" or "monoclonal" to indicate the nature of the antibodies. In cases where a monoclonal antibody is available from the Developmental Studies Hybridoma Bank in Iowa, a link to the DSHB website is provided in the Commercially Available Antibodies section.

FlyBase also lists antibody resources.

Cell Line Information

Publicly Available Cell Lines Links to FlyBase reports for cell lines available from the Drosophila Genomics Resource Center or commercial sources
Other Stable Cell Lines Contains comments about stable cell lines reported in publications that were generated to study a gene via knockout, over-expression, tagging or some other method.

Other Comments

Miscellaneous free text comments about the gene.

Relationship to Other Genes

Source for database merge of A statement indicating that two (or more) gene records have been merged into a single gene record. The statement consists of the valid symbols of the genes at the time of the merge, prefixed with "Source for merge of: ", followed by the publication that was the source of the merge.
Member gene of If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".

This field is displayed in the Gene Report for the individual member of the cluster and lists the gene symbol of the generic record, representing the whole cluster, that the gene is a member of. Clicking on the gene symbol will take you to the Gene Report for the generic record representing the whole cluster.

This field is only displayed in an individual Gene Report if it contains data.

Component gene(s) If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".

This field is displayed in the Gene Report for the generic record, representing the whole cluster, and lists the gene symbols of the individual members of the cluster. Clicking on a gene symbol will take you to the Gene Report for individual member of the cluster.

This field is only displayed in an individual Gene Report if it contains data.

Encoded by This field is typically displayed in a Gene Report for genes encoded by natural transposons, and lists the symbol of the natural transposon that encodes the gene. Clicking on the symbol will take you to the Report for the natural transposon.

This field is only displayed in an individual Gene Report if it contains data.

Additional comments Free text comments about the relationship of the gene to other genes or groups of alleles.

Nomenclature History

Source for database identity of A statement indicating that the symbol used in FlyBase for the gene has been changed. The statement consists of the new symbol and previously used symbol of the gene at the time of the rename, prefixed with "Source for identity of: ", followed by the publication that was the source of the change.
Nomenclature comments Explanation for changing the symbol/name of a previously named gene, such as a change based on the preferred usage by the community, rationalizing nomenclature within a gene family, or because a symbol/name contravenes our nomenclature rules. Such changes are usually actioned directly by FlyBase, though may be the result of information in a publication (e.g. paper or personal communication).
Etymology The explanation behind the gene name as reported by the authors.

Synonyms & Secondary IDs

Reported As

Symbol Synonym A list of symbols that have been used in the literature, or by FlyBase, to describe the gene.
Name Synonym A list of names that have been used in the literature, or by FlyBase, to describe the gene.

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the gene.

If a gene has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.

Datasets

A list of datasets in which the gene was either a key experimental variable, or in which the gene was a key result.

Study focus

Datasets in which the gene was a key experimental variable.

Column heading Description
Experimental Role How the gene was involved in the experimental design. For example, the gene may have been an "RNAi_target", or its product may have been a "bait_protein" for some ChIP study.
Project The name of the project (dataset), which links to the FlyBase "project" report (more detailed reports for related biosamples, assays and results therein).
Project Type The type of project. For example, "genome binding" or "transcriptome"
Title The project's title, which provides a very short description of the study.

Study result

Coming soon. This section will document studies in which the gene is a key "hit" in some screen or analysis.

External Crossreferences & Linkouts

A list of links to external databases for the gene. These links may also be present in other sections of the Gene Report, where appropriate. The Sequence Crossreferences and Other Crossreferences sections contain accession numbers which are FlyBase curated links. The Linkouts section contains linkouts to other relevant resources. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.

The Sequence Crossreferences section contains accession numbers from the following databases:


NCBI Gene - Integrated gene report at NCBI

GenBank - GenBank entries at NCBI

RefSeq - RefSeq entry at NCBI

UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot (reviewed) entry

UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL (unreviewed) entry

UniProtKB/GCRP - UniProt Knowledgebase, Gene-Centric Reference Proteome (GCRP) entry (the 'canonical' isoform representing the product(s) of each protein-coding gene)

References

A list of publications that discuss the gene, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Gene Report.

The icon the top left of the list of publications lists export/download options. 'Filter' allows a text search of the publications associated with the gene and there is a drop-down 'Sort by' option to order publications.

Where available, a thumbnail image of the graphical abstract of the reference is shown to the right of the citation. Clicking on this shows the full size image in a pop-up window, which is itself hyperlinked to the relevant webpage on the journal's website.

The default view of publications for protein-coding genes is the Representative Publications field. This aims to display papers (up to 100) that are most likely to contain the most information on the gene. These publications are identified and scored using an algorithm that assesses the amount and type of data within FlyBase attached to each gene, from each publication. The annotation data being assessed includes (in order of significance): the presence of the gene name/symbol in the title/abstract, the number of Gene Ontology annotations, the number of mutant alleles, the presence of antibody data and the presence of expression data.

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