Skip to main content
SpringerLink
Log in

Using FlyBase, a Database of Drosophila Genes and Genomes

  • Protocol
  • First Online:
Book cover Drosophila

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1478))

Abstract

For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic, and high-throughput technologies add to the quantity and diversity of available data and resources.

FlyBase has taken several approaches to respond to these changes in the research landscape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets, or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.

This chapter provides an overview of the data content, organization, and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 139.00
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Drysdale R, FlyBase Consortium (2008) FlyBase: a database for the Drosophila research community. Methods Mol Biol 420:45–59

    Article  CAS  PubMed  Google Scholar 

  2. McQuilton P, St Pierre SE, Thurmond J et al (2012) FlyBase 101—the basics of navigating FlyBase. Nucleic Acids Res 40:D706–D714

    Article  CAS  PubMed  Google Scholar 

  3. Marygold SJ, Leyland PC, Seal RL et al (2013) FlyBase: improvements to the bibliography. Nucleic Acids Res 41:D751–D757

    Article  CAS  PubMed  Google Scholar 

  4. Wilson RJ, Goodman JL, Strelets VB et al (2008) FlyBase: integration and improvements to query tools. Nucleic Acids Res 36:D588–D593

    Article  CAS  PubMed  Google Scholar 

  5. Tweedie S, Ashburner M, Falls K et al (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37:D555–D559

    Article  CAS  PubMed  Google Scholar 

  6. Kriventseva EV, Tegenfeldt F, Petty TJ et al (2015) OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res 43:D250–D256

    Article  PubMed  Google Scholar 

  7. Cunningham F, Amode MR, Barrell D et al (2015) Ensembl 2015. Nucleic Acids Res 43:D662–D669

    Article  PubMed  Google Scholar 

  8. Gray KA, Yates B, Seal RL et al (2015) Genenames.org: the HGNC resources in 2015. Nucleic Acids Res 43:D1079–D1085

    Article  PubMed  Google Scholar 

  9. OMIM®: Online Mendelian Inheritance in Man®. http://omim.org

  10. Hu Y, Flockhart I, Vinayagam A et al (2011) An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 12:357

    Article  PubMed  PubMed Central  Google Scholar 

  11. St Pierre SE, Ponting L, Stefancsik R et al (2014) FlyBase 102—advanced approaches to interrogating FlyBase. Nucleic Acids Res 42:D780–D788

    Article  CAS  PubMed  Google Scholar 

  12. Morgan TH (1910) Sex limited inheritance in Drosophila. Science 32:120–122

    Article  CAS  PubMed  Google Scholar 

  13. Osumi-Sutherland D, Marygold SJ, Millburn GH et al (2013) The Drosophila phenotype ontology. J Biomed Semantics 4:30

    Article  PubMed  PubMed Central  Google Scholar 

  14. Costa M, Reeve S, Grumbling G et al (2013) The Drosophila anatomy ontology. J Biomed Semantics 4:32

    Article  PubMed  PubMed Central  Google Scholar 

  15. Mohr SE, Hu Y, Kim K et al (2014) Resources for functional genomics studies in Drosophila melanogaster. Genetics 197:1–18

    Article  PubMed  PubMed Central  Google Scholar 

  16. Kibbe WA, Arze C, Felix V et al (2015) Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res 43:D1071–D1078

    Article  PubMed  Google Scholar 

  17. Millburn GH, Crosby MA, Gramates LS et al (2016) FlyBase portals to disease model research in Drosophila. Dis Model Mech 9:245–252

    Article  PubMed  PubMed Central  Google Scholar 

  18. Tomancak P, Beaton A, Weiszmann R et al (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 3, RESEARCH0088

    Article  PubMed  PubMed Central  Google Scholar 

  19. Graveley BR, Brooks AN, Carlson JW et al (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471:473–479

    Article  CAS  PubMed  Google Scholar 

  20. Robinson SW, Herzyk P, Dow JA et al (2013) FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. Nucleic Acids Res 41:D744–D750

    Article  CAS  PubMed  Google Scholar 

  21. Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  PubMed  Google Scholar 

  22. modENCODE Consortium, Roy S, Ernst J et al (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787–1797

    Article  Google Scholar 

  23. Kumar S, Konikoff C, Van Emden B et al (2011) FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics 27:3319–3320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Combs PA, Eisen MB (2013) Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. PLoS One 8:e71820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Bean DM, Heimbach J, Ficorella L et al (2014) esyN: network building, sharing and publishing. PLoS One 9, e106035

    Article  PubMed  PubMed Central  Google Scholar 

  26. Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R et al (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res 43:D470–D478

    Article  PubMed  Google Scholar 

  27. Murali T, Pacifico S, Yu J et al (2011) DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res 39:D736–D743

    Article  CAS  PubMed  Google Scholar 

  28. Wiles AM, Doderer M, Ruan J et al (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol 4:36

    Article  PubMed  PubMed Central  Google Scholar 

  29. Guruharsha KG, Rual JF, Zhai B et al (2011) A protein complex network of Drosophila melanogaster. Cell 147:690–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Kwon Y, Vinayagam A, Sun X et al (2013) The Hippo signaling pathway interactome. Science 342:737–740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ozkan E, Carrillo RA, Eastman CL et al (2013) An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell 154:228–239

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. dos Santos G, Schroeder AJ, Goodman JL et al (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res 43:D690–D697

    Article  PubMed  Google Scholar 

  33. Hoskins RA, Carlson JW, Wan KH et al (2015) The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 25:445–458

    Article  PubMed  PubMed Central  Google Scholar 

  34. Matthews BB, Dos Santos G, Crosby MA et al (2015) Gene model annotations for Drosophila melanogaster: impact of high-throughput data. G3 (Bethesda) 5:1721–1736

    Article  Google Scholar 

  35. Daines B, Wang H, Wang L et al (2011) The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res 21:315–324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Batut P, Dobin A, Plessy C et al (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23:169–180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Drosophila 12 Genomes Consortium, Clark AG, Eisen MB et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218

    Article  Google Scholar 

  38. The NCBI Eukaryotic Genome Annotation Pipeline. http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/

  39. Crosby MA, Gramates LS, Dos Santos G et al (2015) Gene model annotations for Drosophila melanogaster: the rule-benders. G3 (Bethesda) 5:1737–1749

    Article  Google Scholar 

  40. GMOD: the Generic Model Organism Database project. http://gmod.org/wiki/Main_Page

  41. Stein LD (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform 14:162–171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Berger C, Harzer H, Burkard TR et al (2012) FACS purification and transcriptome analysis of Drosophila neural stem cells reveals a role for Klumpfuss in self-renewal. Cell Rep 2:407–418

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Pfeiffer BD, Jenett A, Hammonds AS et al (2008) Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A 105:9715–9720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kvon EZ, Kazmar T, Stampfel G et al (2014) Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512:91–95

    CAS  PubMed  Google Scholar 

  45. Jenett A, Rubin GM, Ngo TT et al (2012) A GAL4-driver line resource for Drosophila neurobiology. Cell Rep 2:991–1001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mackay TF, Richards S, Stone EA et al (2012) The Drosophila melanogaster Genetic Reference Panel. Nature 482:173–178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Attrill HL, Falls K, Goodman JL et al (2016) FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res 44:D786–D792 doi:10.1093/nar/gkv1046

    Article  PubMed  Google Scholar 

  48. Harris TW, Baran J, Bieri T et al (2014) WormBase 2014: new views of curated biology. Nucleic Acids Res 42:D789–D793

    Article  CAS  PubMed  Google Scholar 

  49. Flockhart IT, Booker M, Hu Y et al (2012) FlyRNAi.org—the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res 40:D715–D719

    Article  CAS  PubMed  Google Scholar 

  50. Cook RK, Deal ME, Deal JA et al (2010) A new resource for characterizing X-linked genes in Drosophila melanogaster: systematic coverage and subdivision of the X chromosome with nested, Y-linked duplications. Genetics 186:1095–1109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Bunt SM, Grumbling GB, Field HI et al (2012) Directly e-mailing authors of newly published papers encourages community curation. Database (Oxford) 2012:bas024

    Article  Google Scholar 

Download references

Acknowledgements

FlyBase is funded by the National Human Genome Research Institute at the U.S. National Institutes of Health (#U41HG000739, PI W.M. Gelbart) and the U.K. Medical Research Council (#G1000968, PI N.H. Brown). Support is also provided by the Indiana Genomics Initiative and the National Science Foundation through XSEDE resources provided by Indiana University. At the time of writing, the FlyBase Consortium included William Gelbart, Norbert Perrimon, Cassandra Extavour, Kris Broll, Madeline Crosby, Gilberto dos Santos, David Emmert, Sian Gramates, Kathleen Falls, Beverley Matthews, Susan Russo Gelbart, Andrew Schroeder, Christopher Tabone, Pinglei Zhou, Mark Zytkovicz; Nicholas Brown, Giulia Antonazzo, Helen Attrill, Marta Costa, Steven Marygold, Gillian Millburn, Laura Ponting, Alix Rey, Nicole Staudt, Raymund Stefancsik, Jose-Maria Urbano; Thomas Kaufman, Josh Goodman, Gary Grumbling, Victor Strelets, Jim Thurmond; Richard Cripps, Maggie Werner-Washburne, Phillip Baker.

DedicationWe wish to mark the passing of our colleague and one of FlyBase’s founders, Dr. William Gelbart, who continued in his role of PI until his death. Bill’s leadership, enthusiasm, insight and humor will be greatly missed.

Author information

Authors and Affiliations

  1. Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

    Steven J. Marygold

  2. The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA

    Madeline A. Crosby

  3. Department of Biology, Indiana University, Bloomington, IN, 47405, USA

    Joshua L. Goodman

Authors
  1. Steven J. Marygold
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Madeline A. Crosby
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joshua L. Goodman
    View author publications

    You can also search for this author in PubMed Google Scholar

Consortia

The FlyBase Consortium

Corresponding author

Correspondence to Steven J. Marygold .

Editor information

Editors and Affiliations

  1. Institute of Genetics, Technische Universität Dresden, Dresden, Germany

    Christian Dahmann

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Marygold, S.J., Crosby, M.A., Goodman, J.L., The FlyBase Consortium. (2016). Using FlyBase, a Database of Drosophila Genes and Genomes. In: Dahmann, C. (eds) Drosophila. Methods in Molecular Biology, vol 1478. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6371-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6371-3_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6369-0

  • Online ISBN: 978-1-4939-6371-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation