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What's New in Flybase

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What's New in Flybase What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • GAL4 search • Gene Snapshots • New weBsite: FlyBase 2.0 • Gene Groups • Gene2Function • Orthologs • Alliance of Genome Resources • Human Disease Models Outline 1. Recent additions to FlyBase 2. New features in FlyBase 2.0 3. Multi-species dataBases 4. Further information/feedBack Outline 1. Recent additions to FlyBase 2. New features in FlyBase 2.0 3. Multi-species dataBases 4. Further information/feedBack JBrowse Gene Snapshots Epidermal growth factor receptor (Egfr) is the transmembrane tyrosine kinase receptor for signaling ligands in the TGFα family (grk, spi, vn, and Krn), which utilises the intracellular MAP kinase pathway. Egfr roles include growth regulation, cell survival and developmental patterning. Gene Groups • gene products sharing molecular function (kinases, tRNAs…) • gene families (actins, odorant receptors…) • suBunits of complexes (riBosome, spliceosome…) Gene Group Reports Manually written description of group, with notes List of members, with export to: 1. Hit-list 2. Batch Download 3. Orthologs tool Links to external resources Orthology search tool Orthology search tool Orthology search results Human Disease Model data Human Disease Model Reports Manually written summary of disease and model Links to related diseases/fly models List of fly stocks used in model ‘GAL4 etc.’ search tool ‘GAL4 etc.’ search results Community Interactions Outline 1. Recent additions to FlyBase 2. New features in FlyBase 2.0 3. Multi-species dataBases 4. Further information/feedBack New features include: • New/Improved tools – New hit-list management – Sequence Downloader – Revised Jump-to-Gene/Search Box • Enhanced Report pages – Navigation panel – GO summary riBBons (Gene Report) – Protein domain graphics (Gene/Polypeptide Report) – Reference filtering • Mobile device friendly New hit-lists New hit-lists New hit-lists New hit-lists New hit-lists New hit-lists Revised Gene Reports Revised Gene Reports Revised Gene Reports Revised Gene Reports Revised Jump to Gene/Search Outline 1. Recent additions to FlyBase 2. New features in FlyBase 2.0 3. Multi-species dataBases 4. Further information/feedBack Fly Worm Gene Gene Mouse/ Yeast Rat Gene Gene Human Gene Frog Fish Gene Gene www.gene2function.org Alliance of Genome Resources (AGR) • Current members: – Saccharomyces Genome Database (SGD) – WormBase – FlyBase – Zebrafish Information Network (ZFIN) – Rat Genome Database (RGD) – Mouse Genome Informatics (MGI) – Gene Ontology Consortium • Mission: “To develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease” • 1st public release due October 2017 – Press release etc – Basic gene data, genome browser, GO annotations, disease associations – Prominent links from FlyBase pages to AGR Outline 1. Recent additions to FlyBase 2. New features in FlyBase 2.0 3. Multi-species dataBases 4. Further information/feedBack Further information Acknowledgements & funding FB-Harvard (USA): FB-Cambridge (UK): FB-Indiana (USA): Norbert Perrimon Nick Brown Thomas Kaufman Julie Agapite Giulia Antonazzo Brian Calvi Kris Broll Helen Attrill Bryon Czoch Lynn Crosby Silvie Fexova Josh Goodman Gil dos Santos Phani Garapati Gary GrumBling David Emmert Alex Holmes Victor Strelets L. Sian Gramates Tamsin Jones Jim Thurmond Kathleen Falls Aoife Larkin Beverley Matthews Steven Marygold FB-New Mexico (USA): Susan Russo Gelbart Gillian Millburn Richard Cripps Christopher TaBone Alix Rey Maggie Werner- Pinglei Zhou Vitor Trovisco Washburne Mark Zytkovicz Pepe Urbano Phillip Baker Funding: NHGRI at the U.S. National Institutes of Health (U41HG000739) UK Medical Research Council (G1000968) MARRVEL • Model organism Aggregated Resources for Rare Variant ExpLoration • MARRVEL allows users to search multiple public variant databases simultaneously and provides a unified interface to facilitate the search process. MIST • Molecular Interaction Search Tool • MIST is a comprehensive resource of molecular interactions for several species, including fly, mouse and human. You can mine known physical interactions and infer interactions using other supportive evidence. .
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