Advertisement

Using FlyBase to Find Functionally Related Drosophila Genes

  • Alix J. ReyEmail author
  • Helen Attrill
  • Steven J. Marygold
  • The FlyBase Consortium
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1757)

Abstract

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 words

FlyBase Drosophila D. melanogaster Database Functionally related genes Gene Ontology Protein domain Gene group 

Notes

Acknowledgments

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.

References

  1. 1.
    Gramates LS, Marygold SJ, Santos GD, Urbano JM, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P, FlyBase Consortium (2017) FlyBase at 25: looking to the future. Nucleic Acids Res 45(D1):D663–D671.  https://doi.org/10.1093/nar/gkw1016 CrossRefPubMedGoogle Scholar
  2. 2.
    Marygold SJ, Crosby MA, Goodman JL, FlyBase Consortium (2016) Using FlyBase, a database of Drosophila genes and genomes. Methods Mol Biol 1478:1–31.  https://doi.org/10.1007/978-1-4939-6371-3_1 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    The Gene Ontology C (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 45(D1):D331–D338.  https://doi.org/10.1093/nar/gkw1108 CrossRefGoogle Scholar
  4. 4.
    Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztanyi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45(D1):D190–D199.  https://doi.org/10.1093/nar/gkw1107 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Gaudet P, Livstone MS, Lewis SE, Thomas PD (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform 12(5):449–462.  https://doi.org/10.1093/bib/bbr042 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ, FlyBase Consortium (2016) FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res 44(D1):D786–D792.  https://doi.org/10.1093/nar/gkv1046 CrossRefPubMedGoogle Scholar
  7. 7.
    Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J, FlyBase Consortium (2016) Exploring FlyBase data using QuickSearch. Curr Protoc Bioinformatics 56(1):31 31–31 31 23.  https://doi.org/10.1002/cpbi.19 CrossRefGoogle Scholar
  8. 8.
    St Pierre SE, Ponting L, Stefancsik R, Mcquilton P, FlyBase Consortium (2014) FlyBase 102—advanced approaches to interrogating FlyBase. Nucleic Acids Res 42(Database issue):D780–D788.  https://doi.org/10.1093/nar/gkt1092 CrossRefPubMedGoogle Scholar
  9. 9.
    Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N, Mohr SE (2011) An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 12:357.  https://doi.org/10.1186/1471-2105-12-357 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Yates B, Braschi B, Gray KA, Seal RL, Tweedie S, Bruford EA (2017) Genenames.org: the HGNC and VGNC resources in 2017. Nucleic Acids Res 45(D1):D619–D625.  https://doi.org/10.1093/nar/gkw1033 CrossRefPubMedGoogle Scholar
  11. 11.
    Ratheesh Kumar R, Nagarajan NS, PA S, Sinha D, Veedin Rajan VB, Esthaki VK, D'Silva P (2012) HSPIR: a manually annotated heat shock protein information resource. Bioinformatics 28(21):2853–2855.  https://doi.org/10.1093/bioinformatics/bts520 CrossRefGoogle Scholar
  12. 12.
    Nakao A, Yoshihama M, Kenmochi N (2004) RPG: the Ribosomal Protein Gene database. Nucleic Acids Res 32(Database issue):D168–D170.  https://doi.org/10.1093/nar/gkh004 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37(Database issue):D555–D559.  https://doi.org/10.1093/nar/gkn788 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Alix J. Rey
    • 1
    Email author
  • Helen Attrill
    • 1
  • Steven J. Marygold
    • 1
  • The FlyBase Consortium
  1. 1.Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK

Personalised recommendations