Using FlyBase to Find Functionally Related Drosophila Genes
For more than 25 years, FlyBase (flybase.org) has served as an online database of biological information on the genus Drosophila, concentrating on the model organism D. melanogaster. Traditionally, FlyBase data have been organized and presented at a gene-by-gene level, which remains a useful perspective when the object of interest is a specific gene or gene product. However, in the modern era of a fully sequenced genome and an increasingly characterized proteome, it is often desirable to compile and analyze lists of genes related by a common function. This may be achieved in FlyBase by searching for genes annotated with relevant Gene Ontology (GO) terms and/or protein domain data. In addition, FlyBase provides preassembled lists of functionally related D. melanogaster genes within “Gene Group” reports. These are compiled manually from the published literature or expert databases and greatly facilitate access to, and analysis of, established gene sets. This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their further analysis and processing.
Key wordsFlyBase Drosophila D. melanogaster Database Functionally related genes Gene Ontology Protein domain Gene group
FlyBase is funded by the National Human Genome Research Institute at the US National Institutes of Health (#U41HG000739, PI N. Perrimon) and the UK Medical Research Council (#MR/N030117/1, PI N.H. Brown). At the time of writing, the FlyBase Consortium included: Norbert Perrimon, Julie Agapite, Kris Broll, Madeline Crosby, Gilberto dos Santos, David Emmert, Sian Gramates, Kathleen Falls, Beverley Matthews, Susan Russo Gelbart, Christopher Tabone, Pinglei Zhou, Mark Zytkovicz; Nicholas Brown, Giulia Antonazzo, Helen Attrill, Silvie Fexova, Phani Garapati, Tamsin Jones, Aoife Larkin, Steven Marygold, Gillian Millburn, Alix Rey, Vitor Trovisco, Jose-Maria Urbano; Thomas Kaufman, Bryon Czoch, Josh Goodman, Gary Grumbling, Victor Strelets, Jim Thurmond; Richard Cripps, Maggie Werner-Washburne, Phillip Baker.
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