FlyBase Gene Group Reports
We are pleased to provide new ‘Gene Group Reports’ as of the FB2015_02 release of FlyBase. These Reports bring 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 (WormBase) and humans (HGNC). The current list of Gene Groups in FlyBase can be viewed here, and these may be searched via the Simple tab of QuickSearch or navigated to via the new ‘Gene Group Membership’ section of a Gene Report. (More groups will be added in future FlyBase releases.) Gene Group Reports will greatly aid access to related sets of genes and their associated data in FlyBase, for new and experienced users alike.
Importantly, all Gene Groups in FlyBase are based on published literature and 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. Other useful sections of the Gene Group Report include: a definition of the group; comments on any ‘edge cases’ where the inclusion/exclusion of a particular gene within the group is unclear or disputed; and a list of ‘key Gene Ontology terms’ that largely define the group and which are used to annotate most/all member genes.
We would like to thank our recently formed ‘FlyBase Community Advisory Group (FCAG)’ for helping determine the final content and format of the Gene Group Reports in a recent survey. (Details of FCAG, and the results of that survey can be found here.) We welcome additional feedback on these new Report pages via the Contact FlyBase form. We also encourage you to use this route to suggest additional Gene Groups we should add.
Note that the Gene Group Reports are the first to showcase a new look to FlyBase Report pages, reflecting improvements in the underlying architecture powering the website and enabling some new functionality, such as the floating ‘Report Sections’ navigator on the right of the page. The new look to Report pages will be harmonized across FlyBase in the coming months.