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3DGenomeWorkshop-OverviewofENCODE
DanGilchristNa<onalHumanGenomeResearchIns<tute
October18,2016
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TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants
3DGenomeWorkshop-OverviewofENCODE
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ENCODETutorialshPps://www.encodeproject.org/tutorials/hPp://www.genome.gov/27553900
ENCODETutorials
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ENCODE:Annota<ngthenon-codinggenome
Vastmajorityofcommondiseaseassocia<onsandheritabilitylieoutsideofcodingregionsNon-codingvariantsknowntocausehumandiseasesandalterhumantraits(FXS,ALS)
Stamatoyannopoulos,Science337:1190,2012
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GoalsofENCODE
Iden<fyallcandidatefunc<onalelementsinthehumanandmousegenomes
Promoters,enhancers,transcribedregionsMakeresourcefreelyavailabletothecommunityforuseinstudiesof:
Gene<cbasisofdisease
Generegula<onComputa<onaltooldevelopment
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ENCODEDataTypes
1000sofdatasets100sofbiosamples
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TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants
3DGenomeWorkshop-OverviewofENCODE
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ENCODEPortal–Unrestricteddataaccess
hPps://encodeproject.org
Selectdatasets
Clicktodownloadorvisualize
Dataalsoavailablethroughprograma<cwebservices
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TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants
3DGenomeWorkshop-OverviewofENCODE
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ENCODEAnnota<ons–theEncyclopedia
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TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants
3DGenomeWorkshop-OverviewofENCODE
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ToolsforVariantAnnota<on–FunSeq2
hPp://funseq2.gersteinlab.org/Fu,Khurana,Gerstein,GenomeBiology(15)102014
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ToolsforVariantAnnota<on-RegulomeDB
hPp://regulomedb.org/Boyle,Cherry,Snyder,GenomeResearch22-1790,2012
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ToolsforVariantAnnota<on-HaploReg
www.broadins<tute.org/mammals/haploreg/WardandKellis,NucleicAcidsResearch40-D930,2011
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Comingsoon–ENCODEElementVisualizer!!!
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Comingsoon–NextPhaseofENCODE
Star<ngin2017ElementmappinginnormalanddiseasesamplesCharacterizingfunc<onofcandidateelementsLikelytoincludeexpanded3Ddatasets
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ENCODEatASHG2016
ChatwithENCODEDataCoordina<onCenterandNHGRIENCODEStaff
NHGRIBooth#5172-3PMThursday10/20
ENCODEDCCWorkshop-OpenScience:QualityAssuranceandAnalysisofChIP-seqDataUsingtheENCODEUniformProcessingPipeline
BallroomB7:15AMFriday10/21
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EliseFeingold MikePazin18
ENCODEProjectPar<cipants