Research on the model organism Drosophila melanogaster has been facilitated by the development of a number of online databases for the storage and curation of certain biological data.
DroID
editThe Drosophila Interactions Database (DroID) is an online database of Drosophila gene and protein interactions.[1] It was developed by Russell L. Finley's laboratory at Wayne State University School of Medicine in 2008 and has been funded by the National Human Genome Research Institute, National Institutes of Health's National Center for Research Resources, Michigan Proteome Consortium, and Wayne State University.[2][3]
FlyBase
editFlyBase is the major online database for scientists who work on Drosophila.[4] It contains genome data for various Drosophila species, gene annotations, gene function predictions, and a variety of experimental data that can be overlaid over the genome.[5] FlyBase was developed in 1992 by Michael Ashburner at the University of Cambridge, but is now run by a consortium of groups from Harvard University, University of Cambridge, Indiana University, and the University of New Mexico.[6][5]
FlyFactorSurvey
editFlyFactorSurvey is a database of Drosophila transcription factors determined using the bacterial one-hybrid system.[7] It was developed by the laboratories of Michael H. Brodsky and Scot Wolfe at the University of Massachusetts Medical School in 2011, and was funded by the National Human Genome Research Institute[8]
FlyMine
editFlyMine is a database of transcription, protein expression, and other protein data for Drosophila and Anopheles species.[9] It was originally developed by Gos Micklem's group at Cambridge University in 2007.[10] FlyMine is funded primarily by Wellcome Trust, with elements of the database supported by the National Human Genome Research Institute and the Biotechnology and Biological Sciences Research Council.[11]
OnTheFly
editOnTheFly is a database of D. melanogaster transcription factors and the DNA sequences they bind.[12][13] It was developed by the laboratory of Barry Honig at Columbia University Medical School in 2013.[12]
REDfly
editREDfly (Regulatory Element Database) is a database of Drosophila cis-regulatory elements.[14] It was developed by the laboratory of Marc S. Halfon at the University of Buffalo in 2006, and has been funded by the National Science Foundation and the National Institute of General Medical Sciences.[15]
References
edit- ^ "DroID - The Drosophila Interactions Database". Retrieved 10 July 2019.
- ^ Yu, Jingkai; Pacifico, Svetlana; Liu, Guozhen; Finley Jr, Russell L. (2008). "DroID: The Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions". BMC Genomics. 9: 461. doi:10.1186/1471-2164-9-461. PMC 2572628. PMID 18840285.
- ^ "About Us". DroID. Retrieved 10 July 2019.
- ^ St. Pierre, Susan; McQuilton, Peter (2009). "Inside Fly Base: Biocuration as a career". Fly. 3 (1): 112–114. doi:10.4161/fly.3.1.7769. PMC 2837272. PMID 19182544.
- ^ a b Thurmond, Jim; Goodman, Joshua L.; Strelets, Victor B.; Attrill, Helen; Gramates, L Sian; Marygold, Steven J.; Matthews, Beverley B.; Millburn, Gillian; Antonazzo, Giulia; Trovisco, Vitor; Kaufman, Thomas C.; Calvi, Brian R.; Perrimon, Norbert; Gelbart, Susan Russo; Agapite, Julie; Broll, Kris; Crosby, Lynn; Santos, Gilberto dos; Emmert, David; Gramates, L. Sian; Falls, Kathleen; Jenkins, Victoria; Matthews, Beverley; Sutherland, Carol; Tabone, Christopher; Zhou, Pinglei; Zytkovicz, Mark; Brown, Nick; Antonazzo, Giulia; et al. (2019). "Fly Base 2.0: The next generation". Nucleic Acids Research. 47 (D1): D759–D765. doi:10.1093/nar/gky1003. PMC 6323960. PMID 30364959.
- ^ "FlyBase:About". Retrieved 10 July 2019.
- ^ Zhu, Lihua Julie; Christensen Ryan G; Kazemian Majid; Hull Christopher J; Enuameh Metewo Selase; Basciotta Matthew D; Brasefield Jessie A; Zhu Cong; Asriyan Yuna; Lapointe David S; Sinha Saurabh; Wolfe Scot A; Brodsky Michael H (Jan 2011). "FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system". Nucleic Acids Res. 39 (Database issue). England: D111-7. doi:10.1093/nar/gkq858. PMC 3013762. PMID 21097781.
- ^ "FlyFactorSurvey Homepage". UMass. Retrieved 10 July 2019.
- ^ "About FlyMine". 2014-11-17. Retrieved 10 July 2019.
- ^ Lyne, Rachel; Smith, Richard; Rutherford, Kim; Wakeling, Matthew; Varley, Andrew; Guillier, Francois; Janssens, Hilde; Ji, Wenyan; McLaren, Peter; North, Philip; Rana, Debashis; Riley, Tom; Sullivan, Julie; Watkins, Xavier; Woodbridge, Mark; Lilley, Kathryn; Russell, Steve; Ashburner, Michael; Mizuguchi, Kenji; Micklem, Gos (2007). "Fly Mine: An integrated database for Drosophila and Anopheles genomics". Genome Biology. 8 (7): R129. doi:10.1186/gb-2007-8-7-r129. PMC 2323218. PMID 17615057.
- ^ "FlyMine". Retrieved 10 July 2019.
- ^ a b Shazman, Shula; Lee, Hunjoong; Socol, Yakov; Mann, Richard S.; Honig, Barry (2014). "OnTheFly: A database of Drosophila melanogaster melanogastertranscription factors and their binding sites". Nucleic Acids Research. 42 (Database issue): D167–D171. doi:10.1093/nar/gkt1165. PMC 3965123. PMID 24271386.
- ^ "OnTheFly Homepage". Honig Lab. Retrieved 10 July 2019.
- ^ Rivera, John; Keränen, Soile V E; Gallo, Steven M.; Halfon, Marc S. (2019). "REDfly: The transcriptional regulatory element database for Drosophila". Nucleic Acids Research. 47 (D1): D828–D834. doi:10.1093/nar/gky957. PMC 6323911. PMID 30329093.
- ^ "REDfly About Us". REDfly. Retrieved 10 July 2019.