ENCODE:GettingStartedhttps://www.encodeproject.org; https://www.genome.gov/encode/

Updated11October2016,MikePazin;https://www.genome.gov/pages/research/ENCODE/Tutorials/ENCODE_Getting_Started_2016.pdf 1

ENCODEProject:ThegoalsoftheNHGRIENCODEprojectaretoidentifyallcandidatefunctionalelementsinthegenome,andtomakeacatalogofthoseelementsfreelyavailable

ENCODEPortal(https://encodeproject.org)TheENCODEportalhasdatafromover5000humanand1500mouseENCODEexperiments,aswellasresourcesfromotherprojectssuchastheNIHCommonFundEpigenomicsProgram.Searchescanberefinedthroughfacets,anddatacanbedownloadedordisplayedthroughgenomebrowsers.ENCODEmetadataisalsoavailableprogrammaticallyviawebservices.

ENCODEEncyclopedia(https://www.encodeproject.org/data/annotations/)TheENCODEEncyclopediaorganizesthemostsalientanalysisproductsintoannotations,andprovidestoolstosearchandvisualizethem.Groundlevelannotations,suchasthehuman/mousegeneexpressionvisualizershownbelowleft,aretypicallyderiveddirectlyfromtheexperimentaldata.Middlelevelannotations,suchasthehuman/mouseenhancervisualizershownbelowright,integratemultipletypesofexperimentaldataandmultiplegroundlevelannotations.Toplevelannotations,suchasthetoolsRegulomeDB,HaploReg,andFunSeqshownonthenextpage,integrateabroadrangeofexperimentaldataandgroundandmiddlelevelannotations.

ENCODE:GettingStarted(Page2)https://www.encodeproject.org; https://www.genome.gov/encode/

Updated11October2016,MikePazin;https://www.genome.gov/pages/research/ENCODE/Tutorials/ENCODE_Getting_Started_2016.pdf 2

RegulomeDB(http://www.regulomedb.org)IdentifiesDNAfeaturesandregulatoryelementsinnon-codingregionsofthehumangenome.UsesdatafromENCODE,RoadmapEpigenomics,GTEx,GWAScatalog,andotherprojects.AcceptsSNPIDs,genomiccoordinates,BEDfiles,VCFfiles,GFF3files(hg19)asinput,andreturnsinformationabouttheregulatorypotentialandcellspecificityoftheinputregions.PMID:22955989

HaploReg(http://archive.broadinstitute.org/mammals/haploreg/haploreg.php)Exploresannotationsofthenoncodinggenomeatvariantsonhaplotypeblocks,suchascandidateregulatorySNPsatdisease-associatedloci.UsesdatafromENCODE,RoadmapEpigenomics,GTEx,GWAScatalog,GENCODE,1000Genomes,andotherprojects.AcceptsSNPIDsandgenomiccoordinatesasinput,andreturnsinformationabouttheregulatorypotentialandcellspecificityoftheinputregions.PMID:26657631

FunSeq(http://funseq.gersteinlab.org)Annotatesgermlineandsomaticvariants,particularlyinthenoncodingregionsofcancergenomes.UsesdatafromENCODE,RoadmapEpigenomics,GENCODE,and1000Genomes,integratingalltheevidenceintoasingleimpactscoreforavariant.AcceptsBEDorVCFfilesasinput.PMID:25273974