3D Genome Workshop - Overview of ENCODEepigenomegateway.wustl.edu/support/2016ASHG/2016-10-18... · 2016-10-18 · The ENCODE Project 3D Data Access Through the ENCODE Portal The

3DGenomeWorkshop-OverviewofENCODE

DanGilchristNa<onalHumanGenomeResearchIns<tute

October18,2016

TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants

3DGenomeWorkshop-OverviewofENCODE

ENCODETutorialshPps://www.encodeproject.org/tutorials/hPp://www.genome.gov/27553900

ENCODETutorials

ENCODE:Annota<ngthenon-codinggenome

Vastmajorityofcommondiseaseassocia<onsandheritabilitylieoutsideofcodingregionsNon-codingvariantsknowntocausehumandiseasesandalterhumantraits(FXS,ALS)

Stamatoyannopoulos,Science337:1190,2012

GoalsofENCODE

Iden<fyallcandidatefunc<onalelementsinthehumanandmousegenomes

Promoters,enhancers,transcribedregionsMakeresourcefreelyavailabletothecommunityforuseinstudiesof:

Gene<cbasisofdisease

Generegula<onComputa<onaltooldevelopment

ENCODEDataTypes

1000sofdatasets100sofbiosamples

TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants

3DGenomeWorkshop-OverviewofENCODE

ENCODEPortal–Unrestricteddataaccess

hPps://encodeproject.org

Selectdatasets

Clicktodownloadorvisualize

Dataalsoavailablethroughprograma<cwebservices

TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants

3DGenomeWorkshop-OverviewofENCODE

ENCODEAnnota<ons–theEncyclopedia

TheENCODEProject3DDataAccessThroughtheENCODEPortalTheENCODEEncyclopediaToolsforInves<ga<ngGene<cVariants

3DGenomeWorkshop-OverviewofENCODE

ToolsforVariantAnnota<on–FunSeq2

hPp://funseq2.gersteinlab.org/Fu,Khurana,Gerstein,GenomeBiology(15)102014

ToolsforVariantAnnota<on-RegulomeDB

hPp://regulomedb.org/Boyle,Cherry,Snyder,GenomeResearch22-1790,2012

ToolsforVariantAnnota<on-HaploReg

www.broadins<tute.org/mammals/haploreg/WardandKellis,NucleicAcidsResearch40-D930,2011

Comingsoon–ENCODEElementVisualizer!!!

Comingsoon–NextPhaseofENCODE

Star<ngin2017ElementmappinginnormalanddiseasesamplesCharacterizingfunc<onofcandidateelementsLikelytoincludeexpanded3Ddatasets

ENCODEatASHG2016

ChatwithENCODEDataCoordina<onCenterandNHGRIENCODEStaff

NHGRIBooth#5172-3PMThursday10/20

ENCODEDCCWorkshop-OpenScience:QualityAssuranceandAnalysisofChIP-seqDataUsingtheENCODEUniformProcessingPipeline

BallroomB7:15AMFriday10/21

EliseFeingold MikePazin18

ENCODEProjectPar<cipants