FlyBase:Gene Group Report

From FlyBase Wiki
Jump to: navigation, search

Last Updated: 12 December 2017

The ‘Gene Group Report’ brings together genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or some other functional grouping (e.g. Ubiquitin E3 ligases). The main feature of these Reports is a ‘Members’ table that lists the genes comprising the group, arranged into a series of subgroups where appropriate. Buttons are provided to export these member genes to our ‘Batch Download’ tool, if you wish to download associated data (phenotypes, expression data, protein interactions etc.), or to a standard FlyBase HitList, if you want to further refine or analyse the gene list. Also shown are links to equivalent gene groups for other organisms, including worms (http://www.wormbase.org/resources/gene_class#1-0-5) and humans (http://www.genenames.org/cgi-bin/genefamilies/). Gene group data may be searched in FlyBase via the 'Gene Groups' tab of QuickSearch by using the ‘Enter text' box or by clicking on the hyperlinked 'browse’ to access a list of all Gene Groups (see the related video tutorial Finding related genes in FlyBase: Gene Groups). In addition, Gene Report pages contain a section for ‘Gene Group Membership’ and will display hyperlink(s) to matching group(s).

Importantly, all Gene Groups in FlyBase are compiled manually by FlyBase curators, based on published literature. The basis for the membership of each group is clearly attributed: the Members table shows the reference(s) stating that a specific gene is a member of the given Group; a summary of the source material used to compile the group is displayed at the top of the Report; and all source references are given in full at the foot of the page.

General Information

Name The FlyBase full name for the Gene Group.
Symbol The FlyBase symbol for the Gene Group.
Date last reviewed Date that the group was created or last reviewed, in format 'YEAR-MONTH-DAY'.
Species The species for which the Gene Group has been compiled.
FlyBase ID The unique identifier for the FlyBase Gene Group (FBgg number).
Number of members The number of genes in the Gene Group.

Description

Description A short textual description of the group, written by FlyBase curators based on the given reference(s). References are hyperlinked to their respective Reference Report in FlyBase or to PubMed.
Notes on Group Mainly describes any ‘edge cases’ where the inclusion/exclusion of a specific gene is unclear or debated. Also includes other relevant comments, such as the basis for the nomenclature of the member genes (e.g. it follows the yeast or human naming convention).
Source Material Mini-citations of the primary references, hyperlinked to their respective Reference Reports, used to compile the Gene Group. This section also clearly indicates that the Gene Group has been compiled manually by FlyBase curators.

Key Gene Ontology (GO) terms

Molecular Function Term(s) from the Molecular Function branch of the Gene Ontology that are most relevant to the Gene Group, hyperlinked to the respective FlyBase 'Term Report'. This term, or a child of it, is used to annotate most/all member genes.
Biological Process Term(s) from the Biological Process branch of the Gene Ontology that are most relevant to the Gene Group, hyperlinked to the respective FlyBase 'Term Report'. This term, or a child of it, is used to annotate most/all member genes.
Cellular Component Term(s) from the Cellular Component branch of the Gene Ontology that are most relevant to the Gene Group, hyperlinked to the respective FlyBase 'Term Report'. This term, or a child of it, is used to annotate most/all member genes.

Related Gene Groups

Parent group(s) Any immediate parent super-groups within FlyBase are shown here, hyperlinked to their respective Gene Group Report.
Component group(s) Any immediate child sub-groups within FlyBase are shown here, hyperlinked to their respective Gene Group Report.
Other related group(s) Any groups within FlyBase that are related to the current Gene Group but not through a parent-child relationship (e.g. ligands-receptors, enzymes-substrates) are shown here, hyperlinked to their respective Gene Group Report.

Members

The Members table lists all member genes of the current Gene Group and any subgroups - subgroups are partitioned into individual subsections, the title bar of which is hyperlinked to the Gene Group Report for that subgroup. Member genes are listed alphabetically within each subsection

For all members

View Orthologs Runs the list of genes through the QuickSearch Orthologs tool, and displays a list of orthologs from human and several different model organisms.
Export to HitList Export all genes in the Members Table to a standard FlyBase HitList, which allows further refinement and analysis of the gene list.
Export to Batch Download Export all genes in the Members Table to the FlyBase 'Batch Download' tool, which allows bulk download of any associated data fields.

Members Table

Gene Symbol The FlyBase symbol for the gene, hyperlinked to the Gene Report for that gene.
Gene Name The FlyBase full name for the gene.
Also Known As A list of up to five commonly used symbol synonyms for the gene. (This list is made computationally, based on the frequency of alternative symbols that have been curated from the literature.)
Source Material for Membership The reference(s) that state a specific gene is a member of this particular Gene Group, hyperlinked to the Reference Report for that reference.

External Data

Equivalent Group(s) The name and source of any equivalent Gene Group pages for other organisms such as humans (HUGO Gene Nomenclature Committee, HGNC), nematodes (WormBase) or Arabidopsis (The Arabidopsis Information Resource, TAIR), hyperlinked to that particular resource.
Other resource(s) The name of any other specialist websites relevant to the Gene Group, hyperlinked to that resource.

Synonyms and Secondary IDs

Synonyms(s) Alternative commonly used symbols/names used in Drosophila literature and/or the wider field to refer the Gene Group.
Secondary FlyBase ID(s) Any non-current FlyBase Gene Group ID(s) (FBgg numbers) that have been used previously to refer to the Gene Group but which have retired for some reason (e.g. a new FBgg number is assigned if two or more Gene Groups are merged, or if a single Gene Group is split into separate groups).

References

The full citations of all references used to compile the group, organised by publication type, and hyperlinked to their respective Reference Reports.