what’s new in flybase (in its 25th year) · 2017-10-05 · what’s new in flybase (in its 25th...
TRANSCRIPT
![Page 1: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/1.jpg)
What’s new in FlyBase(in its 25th year)
Steven Marygold
• JBrowse• Gene Snapshots• Gene Groups• Orthologs• Human Disease Models
• GAL4 search• New website: FlyBase 2.0• Gene2Function• Alliance of Genome Resources
![Page 2: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/2.jpg)
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
![Page 3: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/3.jpg)
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
![Page 4: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/4.jpg)
![Page 5: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/5.jpg)
![Page 6: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/6.jpg)
JBrowse
![Page 7: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/7.jpg)
Gene Snapshots
Epidermalgrowthfactorreceptor(Egfr)isthetransmembrane tyrosinekinasereceptorforsignalingligandsintheTGFαfamily(grk,spi,vn,andKrn),whichutilises theintracellularMAPkinasepathway.Egfr rolesincludegrowthregulation,cellsurvivalanddevelopmentalpatterning.
![Page 8: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/8.jpg)
Gene Groups• gene products sharing molecular function (kinases, tRNAs…)• gene families (actins, odorant receptors…)• subunits of complexes (ribosome, spliceosome…)
![Page 9: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/9.jpg)
Gene Group Reports
Linkstoexternalresources
Manuallywrittendescriptionofgroup,withnotes
Listofmembers,withexportto:1.Hit-list2.BatchDownload3.Orthologstool
![Page 10: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/10.jpg)
Orthology search tool
![Page 11: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/11.jpg)
Orthology search tool
![Page 12: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/12.jpg)
Orthology search results
![Page 13: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/13.jpg)
Human Disease Model data
![Page 14: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/14.jpg)
Human Disease Model Reports
Linkstorelateddiseases/flymodels
Manuallywrittensummaryofdiseaseandmodel
Listofflystocksusedinmodel
![Page 15: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/15.jpg)
‘GAL4etc.’searchtool
![Page 16: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/16.jpg)
‘GAL4etc.’searchresults
![Page 17: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/17.jpg)
Community Interactions
![Page 18: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/18.jpg)
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
![Page 19: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/19.jpg)
![Page 20: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/20.jpg)
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
![Page 21: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/21.jpg)
New hit-lists
![Page 22: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/22.jpg)
New hit-lists
![Page 23: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/23.jpg)
New hit-lists
![Page 24: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/24.jpg)
New hit-lists
![Page 25: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/25.jpg)
New hit-lists
![Page 26: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/26.jpg)
New hit-lists
![Page 27: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/27.jpg)
Revised Gene Reports
![Page 28: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/28.jpg)
Revised Gene Reports
![Page 29: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/29.jpg)
Revised Gene Reports
![Page 30: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/30.jpg)
Revised Gene Reports
![Page 31: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/31.jpg)
Revised Jump to Gene/Search
![Page 32: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/32.jpg)
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
![Page 33: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/33.jpg)
www.gene2function.org
FlyGene
Mouse/RatGene
FrogGene
FishGene
YeastGene
WormGene
HumanGene
![Page 34: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/34.jpg)
![Page 35: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/35.jpg)
AllianceofGenomeResources(AGR)• Currentmembers:
– SaccharomycesGenomeDatabase(SGD)– WormBase– FlyBase– ZebrafishInformationNetwork(ZFIN)– RatGenomeDatabase(RGD)– MouseGenomeInformatics(MGI)– GeneOntologyConsortium
• Mission:“Todevelopandmaintainsustainablegenomeinformationresourcesthatfacilitatetheuseofdiversemodelorganismsinunderstandingthegeneticandgenomicbasisofhumanbiology,healthanddisease”
• 1st publicreleasedueOctober2017– Pressreleaseetc– Basicgenedata,genomebrowser,GOannotations,diseaseassociations– ProminentlinksfromFlyBase pagestoAGR
![Page 36: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/36.jpg)
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
![Page 37: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/37.jpg)
Further information
![Page 38: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/38.jpg)
Acknowledgements & fundingFB-Indiana (USA):Thomas KaufmanBrian CalviBryon CzochJosh GoodmanGary GrumblingVictor StreletsJim Thurmond
FB-Harvard (USA):Norbert PerrimonJulie AgapiteKris BrollLynn CrosbyGil dos SantosDavid EmmertL. Sian GramatesKathleen FallsBeverley MatthewsSusan Russo GelbartChristopher TabonePinglei ZhouMark Zytkovicz
FB-Cambridge (UK):Nick BrownGiulia AntonazzoHelen AttrillSilvie FexovaPhani GarapatiAlex HolmesTamsin JonesAoife LarkinSteven MarygoldGillian MillburnAlix ReyVitor TroviscoPepe Urbano
FB-New Mexico (USA):Richard CrippsMaggie Werner-WashburnePhillip Baker
Funding:NHGRI at the U.S. National Institutes of Health (U41HG000739)
UK Medical Research Council (G1000968)
![Page 39: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/39.jpg)
MARRVEL• ModelorganismAggregatedResourcesforRareVariantExpLoration
• MARRVELallowsuserstosearchmultiplepublicvariantdatabasessimultaneouslyandprovidesaunifiedinterfacetofacilitatethesearchprocess.
![Page 40: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/40.jpg)
![Page 41: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/41.jpg)
MIST
• MolecularInteractionSearchTool• MISTisacomprehensiveresourceofmolecularinteractionsforseveralspecies,includingfly,mouseandhuman.Youcanmineknownphysicalinteractionsandinferinteractionsusingothersupportiveevidence.
![Page 42: What’s new in FlyBase (in its 25th year) · 2017-10-05 · What’s new in FlyBase (in its 25th year) Steven Marygold • JBrowse • Gene Snapshots • Gene Groups • Orthologs](https://reader036.vdocuments.us/reader036/viewer/2022070723/5f020e547e708231d4025b61/html5/thumbnails/42.jpg)