FlyBase: establishing a Gene Group resource for Drosophila melanogaster

Abstract

Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multi-protein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.

Figure 1.

Gene Group Curation Strategy. A generalized scheme detailing the workflow for producing Gene Groups in FlyBase. See text for details.

Figure 2.

Finding Gene Groups. (A) The QuickSearch ‘Gene Groups’ tab can be searched using a symbol/name of a group (a search for ‘GPCR’ returns 29 hits that contain ‘GPCR’ in the text of the Report) or a member gene (a search for ‘ninaE’ yields 3 hits from the rhodopsin GPCR hierarchy). (B) Clicking on the ‘browse’ link in the ‘Gene Groups’ tab of QuickSearch takes the user to an alphabetical, nested list of all FlyBase Gene Groups. The section shown focuses on the GPCR hierarchy. (C) Gene Group membership is indicated within the ‘Gene Group Membership (FlyBase)’ field (red box) of the ‘Families, Domains and Molecular Function’ section of the Gene Report. In this example, the upper part of the ninaE Gene Report page is shown and the RHODOPSINS Gene Group is displayed.

Figure 3.

The Gene Group Report. The example shown is for the RECEPTOR PROTEIN TYROSINE PHOSPHATASES group. This group has one immediate parent group (PROTEIN TYROSINE PHOSPHATASES), shown in the ‘Related Gene Groups’ subsection. See text for details.