using encode data to interpret disease-associated ...using encode data to interpret...
TRANSCRIPT
![Page 1: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/1.jpg)
UsingENCODEDataToInterpretDisease-associatedGene8c
Varia8on
MikePazinNa8onalHumanGenomeResearchIns8tute,NIH
ENCODEUsersMee8ngJune8,2016
![Page 2: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/2.jpg)
Welcome• Objec8ves
– WewanttotellthecommunityabouttheENCODEresource
– Wewanttohearcommunityexperiencesandsugges8ons
2
EliseFeingold
DanGilchrist
![Page 3: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/3.jpg)
Overview• TheENCODEResource• UseofENCODEtoilluminatetheroleofgene8cvaria8oninhumandisease
• AccessingENCODEmaterials
3
![Page 4: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/4.jpg)
ReadingTheHumanGenomeIsDifficult• Gene8ccodeverypowerfulfor1%ofthehumangenome• Nocorrespondinglypowerfulregulatorycode• Sequenceconserva8oncaniden8fysomecandidatefunc8onal
elements(butnotwhenorwheretheyact)• Regulatoryregionsaren’talwaysinthesameorderasgenetargetsØ Needunbiasedexperimentalinves8ga8on
99 % Non-coding
1 % Coding
IL10 IL19 4
![Page 5: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/5.jpg)
Non-codingDNAIsImportantForDiseaseAndGeneRegula8on
• Vastmajorityofcommondiseaseassocia8onsandheritabilitylieoutsideofprotein-codingregions
• Non-codingDNAvariantsareknowntocausehumandiseasesandalterhumantraits(FXS,ALS)
Func8onalinforma8onisneededtointerprettheroleofgene8cvaria8oninhumandisease,andtoapplygenomicsintheclinic.
5
PMID:22955828,PMID:25439723,PMID:23128226PMID:17477822,PMID:25679767
![Page 6: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/6.jpg)
1,500LeeersOfOur3BillionLeeerGenome
agccaagcagcaaageegctgctgetaeetgtagctceactataectaceeaccaegaaaataegaggaageaetataetctaeeeatataeatataeeatgtaeeaataeactaeacacataaeaeeeatatatatgaagtaccaatgacecceeccagagcaataatgaaaetcacagtatgaaaatggaagaaatcaataaaaeatacgtgacctgtggcgaagtacctatcgtggacaaggtgagtaccatggtgtatcacaaatgctcetccaaagccctctccgcagctcecccceatgacctctcatcatgccagcaeacctccctggaccccetctaagcatgtcetgagaeectaagaaeceatceggcaacatcegtagcaagaaaatgtaaageectgeccagagcctaacaggaceacataetgactgcagtaggcaeataetagctgatgacataataggectgtcatagtgtagatagggataagccaaaatgcaataagaaaaaccatccagaggaaactceeeeeceetceeeeeeccagatggagtctcgcacectctgtcacccgggctggagcgcagtggtgcaatceggctcactgcaacctccacctcctgggecaggtgaectcccacctcagcctcccgagtagtagctggaaeacaggtgcgcgctcccacacctggctaaeeegtaeceagtagagatggggetcaccatgeggccaggctggtctcaaactcctgccctcaggtgatctgcccacceggcctcccagtgegggetacaggcgtgagccaccgcgcctggcctggaggaaactceaacagggaaactaagaaagagegaggctgaggaactggggcatctgggegcectggccagaccaccaggctcegaatcctcccagccagagaaagagetccacaccagccaegeecctctggtaatgtcagcctcatctgegecctaggceacegatatgetgtaaatgacaaaaggctacagagcataggecctctaaaataecececctgtgtcagataegaatacatagaaatacggtctgatgccgatgaaaatgtatcagcectgataaaaggcggaaeataactaccgagtggtgatgctgaagggagacacagcceggatatgcgaggacgatgcagtgctggacaaaaggcaggtatctcaaaagcctggggagccaactcacccaagtaactgaaagagagaaacaaacatcagtgcagtggaagcacccaaggctacacctgaatggtgggaagctcetgctgctatataaaatgaatcaggctcagctactaeaeacactctcctgaagctaaccaacaetcctgcaacaeatgtagace
6
![Page 7: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/7.jpg)
MapsAndAnnota8onHelpUsToUnderstandTheSequence
agccaagcagcaaageegctgctgetaeetgtagctceactataectaceeaccaegaaaataegaggaageaetataetctaeeeatataeatataeeatgtaeeaataeactaeacacataaeaeeeatatatatgaagtaccaatgacecceeccagagcaataatgaaaetcacagtatgaaaatggaagaaatcaataaaaeatacgtgacctgtggcgaagtacctatcgtggacaaggtgagtaccatggtgtatcacaaatgctcetccaaagccctctccgcagctcecccceatgacctctcatcatgccagcaeacctccctggaccccetctaagcatgtcetgagaeectaagaaeceatceggcaacatcegtagcaagaaaatgtaaageectgeccagagcctaacaggaceacataetgactgcagtaggcaeataetagctgatgacataataggectgtcatagtgtagatagggataagccaaaatgcaataagaaaaaccatccagaggaaactceeeeeceetceeeeeeccagatggagtctcgcacectctgtcacccgggctggagcgcagtggtgcaatceggctcactgcaacctccacctcctgggecaggtgaectcccacctcagcctcccgagtagtagctggaaeacaggtgcgcgctcccacacctggctaaeeegtaeceagtagagatggggetcaccatgeggccaggctggtctcaaactcctgccctcaggtgatctgcccacceggcctcccagtgegggetacaggcgtgagccaccgcgcctggcctggaggaaactceaacagggaaactaagaaagagegaggctgaggaactggggcatctgggegcectggccagaccaccaggctcegaatcctcccagccagagaaagagetccacaccagccaegeecctctggtaatgtcagcctcatctgegecctaggceacegatatgetgtaaatgacaaaaggctacagagcataggecctctaaaataecececctgtgtcagataegaatacatagaaatacggtctgatgccgatgaaaatgtatcagcectgataaaaggcggaaeataactaccgagtggtgatgctgaagggagacacagcceggatatgcgaggacgatgcagtgctggacaaaaggcaggtatctcaaaagcctggggagccaactcacccaagtaactgaaagagagaaacaaacatcagtgcagtggaagcacccaaggctacacctgaatggtgggaagctcetgctgctatataaaatgaatcaggctcagctactaeaeacactctcctgaagctaaccaacaetcctgcaacaeatgtagace
7
![Page 8: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/8.jpg)
RicherMapsProvideMoreInforma8on
8
![Page 9: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/9.jpg)
RicherMapsProvideMoreInforma8on
9
![Page 10: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/10.jpg)
RicherMapsProvideMoreInforma8on
10
![Page 11: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/11.jpg)
RicherMapsProvideMoreInforma8on
11
![Page 12: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/12.jpg)
ENCODE:EncyclopediaOfDNAElements
• Iden8fyallcandidatefunc8onalelementsinthegenome
• Makeresourcefreelyavailabletocommunity– gene8cbasisofdisease– generegula8on
12
![Page 13: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/13.jpg)
ENCODEDataTypes
ModifiedfromPLoSBiol9:e1001046,2011Science306:636,200413
![Page 14: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/14.jpg)
ENCODEDataAreCell-TypeSpecific
14Stamatoyannopoulos,Cell154:888,2013
![Page 15: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/15.jpg)
ENCODEAccomplishments• Sharing1000sofdatasets
– Noembargo– Unrestrictedaccess– Highquality– Uniformlyprocessed
• Sharingsohware• Datainteroperability
15
![Page 16: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/16.jpg)
Publica8onsUsingENCODEData
16
HundredsofConsor8umpublica8ons
~1500communitypublica8onsusingENCODEdata:
~675HumanDisease~600BasicBiology~225Methods/SohwareDevelopment
Cancer38%
Allergy,Autoimmunity13%
HumanGene8cs10%
Neurologic,Psychiatric9%
Cardiovascular6%
Metabolic6%
![Page 17: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/17.jpg)
Summary-ENCODEResource
• Freelysharedcatalogofgenomicdataandcandidategenomicfunc8onalelements
• ENCODEisbuiltuponestablishedtechniquesandinterpreta8onsdevelopedforthestudyofgeneregula8on
• ENCODEmapscanbeusedtomakepredic8onsaboutgenomefunc8on
17
![Page 18: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/18.jpg)
Overview
• TheENCODEResource• UseofENCODEtoilluminatetheroleofgene8cvaria8oninhumandisease
• AccessingENCODEmaterials
18
![Page 19: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/19.jpg)
StandardENCODEUseCases:HypothesisGenera8on
19
Majoruse:Hypothesisgenera8onandrefinement• Predic8onofcausalvariants/regulatoryelements
• Predic8onoftargetgenes• Predic8onoftargetcelltypes• Predic8onofupstreamregulators
![Page 20: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/20.jpg)
Predic8onofCausalVariants• Mul8plevariantsmaybeinlinkagedisequilibrium
• Thecausalvariantmaynothavebeentestedduringdatacollec8on
• Mul8plevariantsmaybecausal
20Snyder,GenomeResearch22:1748,2012
![Page 21: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/21.jpg)
Stamatoyannopoulos,Science337:1190,2012
ManyGWASAssocia8onsLieInRegionsAnnotatedByENCODE
AndCFEpigenomicsData
21
![Page 22: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/22.jpg)
1
2
ENCODE/EpigenomicsDataFromHaploReg
www.broadins8tute.org/mammals/haploreg/22 WardandKellis,NucleicAcidsResearch40-D930,2011WorkshopSession3
![Page 23: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/23.jpg)
ENCODEDataFromRegulomeDB
hep://regulomedb.org/23 Cherry,Snyder,GenomeResearch22-1790,2012
1
2
3
WorkshopSession3
![Page 24: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/24.jpg)
heps://www.encodeproject.org/data/annota8ons/
ENCODEcis-elementBrowser
24WorkshopSession3
![Page 25: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/25.jpg)
heps://www.encodeproject.org/data/annota8ons/
ENCODEcis-elementBrowser
25WorkshopSession3
![Page 26: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/26.jpg)
Predic8onofTargetGenes• Regulatoryregionscanoperateonmul8ple,distalgenes
• Thetargetgenecouldbeanon-codingRNA
26 Stamatoyannopoulos,Crawford,Nature489:75,2012
![Page 27: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/27.jpg)
Stamatoyannopoulos,Science337:1190,2012
ManyGWASAssocia8onsArePredictedToBeLinkedToDistalGenes
27
![Page 28: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/28.jpg)
Stamatoyannopoulos,Science337:1190,2012
ManyGWASAssocia8onsArePredictedToBeLinkedToDistalGenes
28
![Page 29: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/29.jpg)
Predic8onofLinkageBetweenRegulatoryElementsandGenes
29hep://dnase.genome.duke.edu
Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013
![Page 30: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/30.jpg)
Predic8onofLinkageBetweenRegulatoryElementsandGenes
30hep://dnase.genome.duke.edu
Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013
![Page 31: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/31.jpg)
Predic8onofLinkageBetweenRegulatoryElementsandGenes
31hep://dnase.genome.duke.edu
Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013
![Page 32: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/32.jpg)
ENCODEcis-elementBrowser
32 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3
![Page 33: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/33.jpg)
ENCODEcis-elementBrowser
33 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3
![Page 34: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/34.jpg)
Predic8onofTargetCellTypes• Somediseasesareknowntoaffectmul8plecelltypes
• Thedefectmaynotbeintrinsictothecelltypewithobviouspathology
• Thediseasee8ologymaynotbecompletelyknown
34
![Page 35: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/35.jpg)
Predic8onofLinkageBetweenRegulatoryElementsandCellType
35hep://dnase.genome.duke.edu
Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013
![Page 36: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/36.jpg)
Predic8onofLinkageBetweenRegulatoryElementsandCellType
hep://regulomedb.org/
36 Cherry,Snyder,GenomeResearch22-1790,2012www.broadins8tute.org/mammals/haploreg/WardandKellis,NucleicAcidsResearch40-D930,2011
WorkshopSession3
![Page 37: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/37.jpg)
ENCODEcis-elementBrowser
37 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3
![Page 38: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/38.jpg)
ENCODEcis-elementBrowser
38 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3
![Page 39: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/39.jpg)
heps://github.com/mauranolab/GWAS_plotsStamatoyannopoulos,Science337:1190,2012
ENCODEAndEpigenomicsDataCanBeUsedToPredictCellTypes
39
![Page 40: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/40.jpg)
Summary-ENCODEUseCases
Majoruse:Hypothesisgenera8onandrefinement• Predic8onofcausalvariants/regulatoryelements• Predic8onoftargetgenes• Predic8onoftargetcelltypes• Predic8onofupstreamregulators
Ø Gene8cv.epigene8cØ Germlinev.soma8c
40
![Page 41: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/41.jpg)
Overview• TheENCODEResource• UseofENCODEbytheresearchcommunity
• AccessingENCODEmaterials
41
WorkshopSession2,1,5
![Page 42: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/42.jpg)
heps://www.encodeproject.org
ENCODEData
42 WorkshopSession2
![Page 43: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/43.jpg)
heps://www.encodeproject.org
ENCODEData
43 WorkshopSession2
![Page 44: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/44.jpg)
heps://www.encodeproject.org
ENCODEData
44 WorkshopSession2
![Page 45: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/45.jpg)
heps://www.encodeproject.org
ENCODEData
45 WorkshopSession2
![Page 46: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/46.jpg)
heps://www.encodeproject.org
ENCODEData
46 WorkshopSession2
![Page 47: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/47.jpg)
heps://www.encodeproject.org
ENCODEData
47 WorkshopSession2
![Page 48: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/48.jpg)
heps://www.encodeproject.org
ENCODEData
48 WorkshopSession2
![Page 49: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/49.jpg)
ENCODEEncyclopedia
49 heps://www.encodeproject.orgWorkshopSession1,5
![Page 50: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/50.jpg)
ENCODEEncyclopedia
50 heps://www.encodeproject.orgWorkshopSession1,5
![Page 51: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/51.jpg)
ENCODEEncyclopedia
51 heps://www.encodeproject.orgWorkshopSession1,5
![Page 52: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/52.jpg)
ENCODEEncyclopedia
52 heps://www.encodeproject.orgWorkshopSession1,5
![Page 53: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/53.jpg)
ENCODEEncyclopedia
53 heps://www.encodeproject.orgWorkshopSession1,5
![Page 54: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/54.jpg)
Publica8ons
heps://www.encodeproject.org54
![Page 55: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/55.jpg)
Publica8ons
heps://www.encodeproject.org55
![Page 56: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/56.jpg)
ENCODEDataStandards
heps://www.encodeproject.org56
![Page 57: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/57.jpg)
ENCODEDataStandards
heps://www.encodeproject.org57
![Page 58: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/58.jpg)
ENCODESohwareTools
heps://www.encodeproject.org58
![Page 59: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/59.jpg)
ENCODESohwareTools
heps://www.encodeproject.org59
![Page 60: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/60.jpg)
Interna8onalHumanEpigenomeConsor8um(IHEC)
• DataPortal:hep://epigenomesportal.ca/ihec/• Goal:Coordinateproduc8onof1000humanepigenomemapsforcellularstatesrelevanttohealthanddiseasehep://ihec-epigenomes.org
• Canviewbyconsor8um,byassay,bycelltype• Datafrom8consor8a
60CEEHRC
![Page 61: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/61.jpg)
Summary-AccessingENCODEResources
• ENCODEportalheps://www.encodeproject.org– Display/downloadENCODEandRoadmapEpigenomicsdata– DataStandards– Sohwaretools– Publica8ons– Encyclopediaprototype
• ENCODEAnalysisTools– RegulomeDBhep://regulomedb.org/– HaploReghep://www.broadins8tute.org/mammals/haploreg/– RegulatoryElementsDatabasehep://dnase.genome.duke.edu– RegulomeDBGWASDatabasehep://www.regulomedb.org/GWAS/
• ENCODETutorials– hep://www.genome.gov/27553900– heps://www.encodeproject.org/tutorials/
hep://www.ncbi.nlm.nih.gov/pubmed/25762420• ENCODEmailinglist:
– heps://mailman.stanford.edu/mailman/lis8nfo/encode-announce• IHECresources
– IHECHomePagehep://ihec-epigenomes.org– IHECDataPortalhep://epigenomesportal.ca/ihec/
61
![Page 62: Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret Disease-associated Gene8c Variaon Mike Pazin Naonal Human Genome Research Ins8tute, NIH ENCODE Users](https://reader034.vdocuments.net/reader034/viewer/2022042808/5f88da27d7da09651e691989/html5/thumbnails/62.jpg)
GoalsOfENCODE• Catalogallfunc8onalelementsinthegenome• Developfreelyavailableresourceforresearchcommunity
ENCODEdataarebeingusedinthestudyofhumandiseaseandbasicbiology
62