FlyBase:Gene Group Report

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.

NOTE: The ‘Gene Group - Pathway Report’ is a sub-category of our Gene Group resource. For documentation on this resource see the Pathway Report 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.

Enzymatic activity

Enzyme name (EC)

Where relevant, the systematic name for the enzyme represented by the Gene Group together with its Enzyme Commission (EC) number. Where an enzymatic Gene Group corresponds to a partial EC number (e.g. GLYCOSYLTRANSFERASES (FBgg0000795) corresponds to EC:2.4.-.-), only the EC number is shown. These data are derived from the Gene Ontology (GO) Molecular Function annotation applied to the Gene Group by using the EC cross-references within the GO. Each EC number is linked to the corresponding page at the ExPASy ENZYME database.

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.

GO ribbon stack

Each row or 'ribbon' is a graphical summary of a gene product's properties and depth of characterization. The data used to populate ribbons 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 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 or clicking on the cell. Some terms may group under more than one cell because the GO allows multiple ancestry. By stacking the ribbons for each gene in the members table, an at-a-glance comparison of member genes is presented. For more details on how the ribbons are generated see Gene Report - Function.

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.