Post on 04-Jun-2020
transcript
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
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
Epidermalgrowthfactorreceptor(Egfr)isthetransmembrane tyrosinekinasereceptorforsignalingligandsintheTGFαfamily(grk,spi,vn,andKrn),whichutilises theintracellularMAPkinasepathway.Egfr rolesincludegrowthregulation,cellsurvivalanddevelopmentalpatterning.
Gene Groups• gene products sharing molecular function (kinases, tRNAs…)• gene families (actins, odorant receptors…)• subunits of complexes (ribosome, spliceosome…)
Gene Group Reports
Linkstoexternalresources
Manuallywrittendescriptionofgroup,withnotes
Listofmembers,withexportto:1.Hit-list2.BatchDownload3.Orthologstool
Orthology search tool
Orthology search tool
Orthology search results
Human Disease Model data
Human Disease Model Reports
Linkstorelateddiseases/flymodels
Manuallywrittensummaryofdiseaseandmodel
Listofflystocksusedinmodel
‘GAL4etc.’searchtool
‘GAL4etc.’searchresults
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
www.gene2function.org
FlyGene
Mouse/RatGene
FrogGene
FishGene
YeastGene
WormGene
HumanGene
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
Outline
1. Recent additions to FlyBase
2. New features in FlyBase 2.0
3. Multi-species databases
4. Further information/feedback
Further information
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)
MARRVEL• ModelorganismAggregatedResourcesforRareVariantExpLoration
• MARRVELallowsuserstosearchmultiplepublicvariantdatabasessimultaneouslyandprovidesaunifiedinterfacetofacilitatethesearchprocess.
MIST
• MolecularInteractionSearchTool• MISTisacomprehensiveresourceofmolecularinteractionsforseveralspecies,includingfly,mouseandhuman.Youcanmineknownphysicalinteractionsandinferinteractionsusingothersupportiveevidence.