Drosophila pp 1-31

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

Using FlyBase, a Database of Drosophila Genes and Genomes

  • Steven J. Marygold
  • Madeline A. Crosby
  • Joshua L. Goodman
  • The FlyBase Consortium

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.

Key words

FlyBase Drosophila Database Genetics Genomics Translational research 

References

  1. 1.
    Drysdale R, FlyBase Consortium (2008) FlyBase: a database for the Drosophila research community. Methods Mol Biol 420:45–59CrossRefPubMedGoogle Scholar
  2. 2.
    McQuilton P, St Pierre SE, Thurmond J et al (2012) FlyBase 101—the basics of navigating FlyBase. Nucleic Acids Res 40:D706–D714CrossRefPubMedGoogle Scholar
  3. 3.
    Marygold SJ, Leyland PC, Seal RL et al (2013) FlyBase: improvements to the bibliography. Nucleic Acids Res 41:D751–D757CrossRefPubMedGoogle Scholar
  4. 4.
    Wilson RJ, Goodman JL, Strelets VB et al (2008) FlyBase: integration and improvements to query tools. Nucleic Acids Res 36:D588–D593CrossRefPubMedGoogle Scholar
  5. 5.
    Tweedie S, Ashburner M, Falls K et al (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37:D555–D559CrossRefPubMedGoogle Scholar
  6. 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–D256CrossRefPubMedGoogle Scholar
  7. 7.
    Cunningham F, Amode MR, Barrell D et al (2015) Ensembl 2015. Nucleic Acids Res 43:D662–D669CrossRefPubMedGoogle Scholar
  8. 8.
    Gray KA, Yates B, Seal RL et al (2015) Genenames.org: the HGNC resources in 2015. Nucleic Acids Res 43:D1079–D1085CrossRefPubMedGoogle Scholar
  9. 9.
    OMIM®: Online Mendelian Inheritance in Man®. http://omim.org
  10. 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 12:357CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    St Pierre SE, Ponting L, Stefancsik R et al (2014) FlyBase 102—advanced approaches to interrogating FlyBase. Nucleic Acids Res 42:D780–D788CrossRefPubMedGoogle Scholar
  12. 12.
    Morgan TH (1910) Sex limited inheritance in Drosophila. Science 32:120–122CrossRefPubMedGoogle Scholar
  13. 13.
    Osumi-Sutherland D, Marygold SJ, Millburn GH et al (2013) The Drosophila phenotype ontology. J Biomed Semantics 4:30CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Costa M, Reeve S, Grumbling G et al (2013) The Drosophila anatomy ontology. J Biomed Semantics 4:32CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Mohr SE, Hu Y, Kim K et al (2014) Resources for functional genomics studies in Drosophila melanogaster. Genetics 197:1–18CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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–D1078CrossRefPubMedGoogle Scholar
  17. 17.
    Millburn GH, Crosby MA, Gramates LS et al (2016) FlyBase portals to disease model research in Drosophila. Dis Model Mech 9:245–252CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Tomancak P, Beaton A, Weiszmann R et al (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 3, RESEARCH0088CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Graveley BR, Brooks AN, Carlson JW et al (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471:473–479CrossRefPubMedGoogle Scholar
  20. 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–D750CrossRefPubMedGoogle Scholar
  21. 21.
    Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628CrossRefPubMedGoogle Scholar
  22. 22.
    modENCODE Consortium, Roy S, Ernst J et al (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787–1797CrossRefGoogle Scholar
  23. 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 27:3319–3320CrossRefPubMedPubMedCentralGoogle Scholar
  24. 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:e71820CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Bean DM, Heimbach J, Ficorella L et al (2014) esyN: network building, sharing and publishing. PLoS One 9, e106035CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R et al (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res 43:D470–D478CrossRefPubMedGoogle Scholar
  27. 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–D743CrossRefPubMedGoogle Scholar
  28. 28.
    Wiles AM, Doderer M, Ruan J et al (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol 4:36CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Guruharsha KG, Rual JF, Zhai B et al (2011) A protein complex network of Drosophila melanogaster. Cell 147:690–703CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Kwon Y, Vinayagam A, Sun X et al (2013) The Hippo signaling pathway interactome. Science 342:737–740CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Ozkan E, Carrillo RA, Eastman CL et al (2013) An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell 154:228–239CrossRefPubMedPubMedCentralGoogle Scholar
  32. 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–D697CrossRefPubMedGoogle Scholar
  33. 33.
    Hoskins RA, Carlson JW, Wan KH et al (2015) The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 25:445–458CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Matthews BB, Dos Santos G, Crosby MA et al (2015) Gene model annotations for Drosophila melanogaster: impact of high-throughput data. G3 (Bethesda) 5:1721–1736CrossRefGoogle Scholar
  35. 35.
    Daines B, Wang H, Wang L et al (2011) The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res 21:315–324CrossRefPubMedPubMedCentralGoogle Scholar
  36. 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 23:169–180CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Drosophila 12 Genomes Consortium, Clark AG, Eisen MB et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218CrossRefGoogle Scholar
  38. 38.
    The NCBI Eukaryotic Genome Annotation Pipeline. http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/
  39. 39.
    Crosby MA, Gramates LS, Dos Santos G et al (2015) Gene model annotations for Drosophila melanogaster: the rule-benders. G3 (Bethesda) 5:1737–1749CrossRefGoogle Scholar
  40. 40.
    GMOD: the Generic Model Organism Database project. http://gmod.org/wiki/Main_Page
  41. 41.
    Stein LD (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform 14:162–171CrossRefPubMedPubMedCentralGoogle Scholar
  42. 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 2:407–418CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Pfeiffer BD, Jenett A, Hammonds AS et al (2008) Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A 105:9715–9720CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Kvon EZ, Kazmar T, Stampfel G et al (2014) Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512:91–95PubMedGoogle Scholar
  45. 45.
    Jenett A, Rubin GM, Ngo TT et al (2012) A GAL4-driver line resource for Drosophila neurobiology. Cell Rep 2:991–1001CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Mackay TF, Richards S, Stone EA et al (2012) The Drosophila melanogaster Genetic Reference Panel. Nature 482:173–178CrossRefPubMedPubMedCentralGoogle Scholar
  47. 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 CrossRefPubMedGoogle Scholar
  48. 48.
    Harris TW, Baran J, Bieri T et al (2014) WormBase 2014: new views of curated biology. Nucleic Acids Res 42:D789–D793CrossRefPubMedGoogle Scholar
  49. 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–D719CrossRefPubMedGoogle Scholar
  50. 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 186:1095–1109CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Bunt SM, Grumbling GB, Field HI et al (2012) Directly e-mailing authors of newly published papers encourages community curation. Database (Oxford) 2012:bas024CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Steven J. Marygold
    • 1
  • Madeline A. Crosby
    • 2
  • Joshua L. Goodman
    • 3
  • The FlyBase Consortium
  1. 1.Department of GeneticsUniversity of CambridgeCambridgeUK
  2. 2.The Biological LaboratoriesHarvard UniversityCambridgeUSA
  3. 3.Department of BiologyIndiana UniversityBloomingtonUSA

Personalised recommendations