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ENCODE and Epigenomics Roadmap Workshop
Workshop Overview13 1 IntroducRon
bull Overview of the projects bull What13 data13 are available bull New features
2 How the scienRfic community has used ENCODE and Roadmap Epigenomics data13
3 InteracRve tutorial bull Commonly asked quesRons about13 data13 access bull QuesRons about13 analyzing the data13 bull We want13 to hear your quesRons
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Project13 goals
NIH Roadmap Epigenomics Program Research to transform our understanding of how epigeneRcs contributes to disease
(hTpcommonfundnihgovepigenomics)13
ENCODE13 (Encyclopedia13 of DNA13 Elements) CreaRng comprehensive high quality catalogs of funcRonal elements in the human and mouse genomes using high-shy‐throughput13 technologies Completed analysis of the genomes of the fruit13 fly and roundworm
(hTpwwwgenomegovencode)13
Common purposes13 1 Create a public resource of data13
bull Experimental data13 available pre-shy‐publicaRon bull Encourage community use of datasets
2 Promote technology development13 bull For epigenomics research bull IdenRficaRon and validaRon of funcRonal elements
3 Development13 of standards bull DefiniRon of metadata13 bull Standards for performing the assaybull Uniform analysis of data13 bull Standards for data13 quality
ENCODEEpigenomics Roadmap Workshop ASHG 2013
What13 data13 types are available RoadmapENCODE13 Epigenomics
ChIP-shy‐seq (transcripRon factors RNA-shy‐bindingproteins)
ChIP-shy‐seq (histone marks)
RNA-shy‐seq
bull
bull bull
bull bull
RNA-shy‐seq aCer shRNAsiRNA knockdown13 bull
DNA methylaRon bull bull
DNAse bull bull
RNA-shy‐binding assays (CLIP-shy‐seq RIP-shy‐seq)13 bull
Enhancer assays bull
5C bull
~3400 ~120 completeTotal data13 datasets epigenomes
ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Workshop Overview13 1 IntroducRon
bull Overview of the projects bull What13 data13 are available bull New features
2 How the scienRfic community has used ENCODE and Roadmap Epigenomics data13
3 InteracRve tutorial bull Commonly asked quesRons about13 data13 access bull QuesRons about13 analyzing the data13 bull We want13 to hear your quesRons
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Project13 goals
NIH Roadmap Epigenomics Program Research to transform our understanding of how epigeneRcs contributes to disease
(hTpcommonfundnihgovepigenomics)13
ENCODE13 (Encyclopedia13 of DNA13 Elements) CreaRng comprehensive high quality catalogs of funcRonal elements in the human and mouse genomes using high-shy‐throughput13 technologies Completed analysis of the genomes of the fruit13 fly and roundworm
(hTpwwwgenomegovencode)13
Common purposes13 1 Create a public resource of data13
bull Experimental data13 available pre-shy‐publicaRon bull Encourage community use of datasets
2 Promote technology development13 bull For epigenomics research bull IdenRficaRon and validaRon of funcRonal elements
3 Development13 of standards bull DefiniRon of metadata13 bull Standards for performing the assaybull Uniform analysis of data13 bull Standards for data13 quality
ENCODEEpigenomics Roadmap Workshop ASHG 2013
What13 data13 types are available RoadmapENCODE13 Epigenomics
ChIP-shy‐seq (transcripRon factors RNA-shy‐bindingproteins)
ChIP-shy‐seq (histone marks)
RNA-shy‐seq
bull
bull bull
bull bull
RNA-shy‐seq aCer shRNAsiRNA knockdown13 bull
DNA methylaRon bull bull
DNAse bull bull
RNA-shy‐binding assays (CLIP-shy‐seq RIP-shy‐seq)13 bull
Enhancer assays bull
5C bull
~3400 ~120 completeTotal data13 datasets epigenomes
ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Project13 goals
NIH Roadmap Epigenomics Program Research to transform our understanding of how epigeneRcs contributes to disease
(hTpcommonfundnihgovepigenomics)13
ENCODE13 (Encyclopedia13 of DNA13 Elements) CreaRng comprehensive high quality catalogs of funcRonal elements in the human and mouse genomes using high-shy‐throughput13 technologies Completed analysis of the genomes of the fruit13 fly and roundworm
(hTpwwwgenomegovencode)13
Common purposes13 1 Create a public resource of data13
bull Experimental data13 available pre-shy‐publicaRon bull Encourage community use of datasets
2 Promote technology development13 bull For epigenomics research bull IdenRficaRon and validaRon of funcRonal elements
3 Development13 of standards bull DefiniRon of metadata13 bull Standards for performing the assaybull Uniform analysis of data13 bull Standards for data13 quality
ENCODEEpigenomics Roadmap Workshop ASHG 2013
What13 data13 types are available RoadmapENCODE13 Epigenomics
ChIP-shy‐seq (transcripRon factors RNA-shy‐bindingproteins)
ChIP-shy‐seq (histone marks)
RNA-shy‐seq
bull
bull bull
bull bull
RNA-shy‐seq aCer shRNAsiRNA knockdown13 bull
DNA methylaRon bull bull
DNAse bull bull
RNA-shy‐binding assays (CLIP-shy‐seq RIP-shy‐seq)13 bull
Enhancer assays bull
5C bull
~3400 ~120 completeTotal data13 datasets epigenomes
ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Common purposes13 1 Create a public resource of data13
bull Experimental data13 available pre-shy‐publicaRon bull Encourage community use of datasets
2 Promote technology development13 bull For epigenomics research bull IdenRficaRon and validaRon of funcRonal elements
3 Development13 of standards bull DefiniRon of metadata13 bull Standards for performing the assaybull Uniform analysis of data13 bull Standards for data13 quality
ENCODEEpigenomics Roadmap Workshop ASHG 2013
What13 data13 types are available RoadmapENCODE13 Epigenomics
ChIP-shy‐seq (transcripRon factors RNA-shy‐bindingproteins)
ChIP-shy‐seq (histone marks)
RNA-shy‐seq
bull
bull bull
bull bull
RNA-shy‐seq aCer shRNAsiRNA knockdown13 bull
DNA methylaRon bull bull
DNAse bull bull
RNA-shy‐binding assays (CLIP-shy‐seq RIP-shy‐seq)13 bull
Enhancer assays bull
5C bull
~3400 ~120 completeTotal data13 datasets epigenomes
ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
What13 data13 types are available RoadmapENCODE13 Epigenomics
ChIP-shy‐seq (transcripRon factors RNA-shy‐bindingproteins)
ChIP-shy‐seq (histone marks)
RNA-shy‐seq
bull
bull bull
bull bull
RNA-shy‐seq aCer shRNAsiRNA knockdown13 bull
DNA methylaRon bull bull
DNAse bull bull
RNA-shy‐binding assays (CLIP-shy‐seq RIP-shy‐seq)13 bull
Enhancer assays bull
5C bull
~3400 ~120 completeTotal data13 datasets epigenomes
ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
How can the data13 be used Hypothesis generaRon and refinement13 of gene regulaRon
bull What13 are the enhancers and promoter regions for a gene bull What13 is the target13 gene for the regulatory regions bull Is the regulaRon specific for certain cell types
Many geneRc findings for human disease map to non-shy‐protein coding regions of the human genome ENCODE idenRfied regions can help develop hypotheses
bull What13 is the causal variant bull What13 is the funcRon of the variant
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE data access
ConsorLum homepage hTpencodeprojectorgbull View metadata protocols and standardsbull Data visualizaRon at hTpgenomeucscedu hTpensemblorg
NCBI hTpwwwncbinlmnihgovbioproject30707 (human)hTpwwwncbinlmnihgovbioproject50617 (mouse)
bull View and download databull Compare samples
modENCODE hTpmodencodeorgbull View and download data
EENNCCOODDEEEEppiiggeennoomimicscs RoRoaaddmamapp WWoorrkksshhoopp AASSHGHG 22001133
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics data13 access ConsorLum13 homepage13 hTproadmapepigenomicsorg bull Genome13 browser13 bull View protocols and standards
NCBI13 hTpncbinlmnihgovepigenomics hTpncbinlmnihgovgeoroadmapepigenomics
bull View and download data13 bull Compare samples
Human13 Epigenome Atlas hTpepigenomeatlasorg bull View data13 on genome or with Atlas gene browser bull Download data13 bull Use13 Genboree Workbench tools
WashU VizHub hTpvizhubwustledu bull Next-shy‐gen browser hTpepigenomegatewaywustledu bull UCSC visualizaRon hub at hTpgenomeucscedu
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Roadmap Epigenomics Mapping ConsorRum
bull Reference Epigenome Mapping Centers Brad Bernstein amp Alex Meissner (Broad) Joe Costello (UCSF)13 Bing13 Ren (UCSD) John Stamatoyannopoulous (Washington)
bull Epigenomics Data13 Analysis and CoordinaRon Center Aleks Milosavljevic (Baylor)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
ENCODE13 ConsorRum ENCODE13 ProducLon13 Centers
Bradley13 Bernstein13 (John Rinn Manolis Kellis)
Thomas13 Gingeras13 (Carrie Davis Roderic Guigo)
Brenton13 Graveley13 (Christopher Burge Xiang-shy‐Dong Fu Eugene Yeo)
Richard Myers (Devin13 Absher Gregory Cooper Shawn Levy FlorenciaPauli Behn Ross Hardison Ali Mortazavi Timothy Reddy Barbara13 Wold)
Bing Ren (Joseph13 Ecker Len13 Pennacchio Axel Visel Wei Wang)
Michael Snyder (Kevin White Sherman Weissman Peggy Farnham)
John Stamatoyannopoulos13 (Ralph Hansen Rajinder Kaul PatrickNavas George Stamatoyannopoulos Piper TreuRng Michael BenderJob Dekker Mark Groudine)13
ENCODE13 Data13 CoordinaLon13 Center
Mike Cherry (Jim Kent)
ENCODE Data Analysis Center
Zhiping Weng (Mark Gerstein Manolis Kellis Roderic Guigo RafaelIrizarry Xiaole Shirley Liu William Stafford Noble)
AddiLonal ENCODE ParLcipants
Timothy Hubbard (Mark Gerstein Roderic Guigo Jen Harrow RachelHarte David Haussler Manolis Kellis Alexandre Reymond StephenSearle Alfonso Valencia)
David Gilbert (Tamer Kahveci)
ENCODE ComputaLonal Analysis Groups
Peter Bickel (Haiyan Huang Leonard Lipovich Bin Yu)
David Gifford (Tommi Jaakkola)13
Sunduz Keles13 (Emery Bresnick13 Colin Dewey)
Robert Klein (ChrisRna13 Leslie Souma13 Raychaudhuri Ross LevineKenneth Offit)13
Jonathan Pritchard (Yoav Gilad)13
Xinshu Xiao
ENCODE13 Technology13 Development13 Groups13
Christopher13 Burge13 (Wendy Gilbert Brenton Graveley Robert13 Horvitz)
Barak13 Cohen and Joseph Corbo
Peggy Farnham (Victor Jin David Jay Segal)
R David Hawkins
ChrisLna Leslie13 (Christopher Mason)
Jason Lieb (Karen Mohlke13 Eran Segal)
Mats Ljungman (Thomas Wilson)
Tarjei Mikkelsen
Jay Shendure and Nadav Ahituv (Michael McManus)
Alexey Wolfson
Guo-shy‐Cheng13 Yuan (Stuart13 Orkin)13
hellip and many senior13 scienLsts postdocs students technicians computer13 scienLsts staLsLcians andadministrators13 in these groups13
Current ENCODE parLcipants13 hNpwwwgenomegov26525220
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Future direcRons
1 Shared metadata13 standard among mulRple projects ENCODE modENCODE Roadmap Epigenomics
2 AnnotaRon of metadata13 using ontologies
3 Biologically intuiRve displays of metadata13
4 Easier idenRficaRon of data13 sets using metadata13
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Biologically relevant13 view of metadataEurie Hong (1462T)
about13 the
Protocols and addiRonal documentaRon
Details describing the biosample
De-shy‐idenRfied informaRon donor
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Using ontologies for searchingVenkat Malladi (1613F)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Contact13 us
encode-shy‐helplistsstanfordedu
encodedcc
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Speakers
GeneLcs and Genomics of Maternal Glycemia During13 Pregnancy13 New Insights13 from13 Genome Wide Mapping and ENCODEWilliam L Lowe Jr MDProfessor of Medicine and Vice Dean for Academic AffairsNorthwestern University
Expression and RegulaLon of Lung FuncLon Genome-shy‐Wide Associated LocusMaen Obeidat13 PhDPost-shy‐doctoral fellow (PI Peter Pare PhD)University of BriRsh Columbia13
Using the Epigenome Roadmap data to analyze geneLc studies of type 2 diabetesVineeta Agarwala (PhD student PI David Altshuler MD PhD Broad InsRtute)Abhishek Sarkar (PhD student PI Manolis Kellis PhD Broad InsRtute)Kyle13 Gaulton (Post-shy‐doctoral fellow PI Mark McCarthy Peter Donnelly Wellcome Trust13 Centre for Human GeneRcs)
ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
Tutorial bull How can ENCODE data13 help with analysis of SNP data13 from
GWAS studies Jill Moore Luke Ward Robert13 Klein bull How can ENCODE data13 help with annotaRon of non-shy‐coding
variants Jill Moore Ekta Khurana Robert13 Klein bull How can ENCODE data13 help idenRfy how my gene of interest13 is
regulated Alon Goren Brian Lee Adam Frankish (single gene level analysis) Ross Hardison
bull What13 can ENCODE data13 tell me about13 my genes expression levels13 Brian Lee Eurie Hong Adam Frankish (single gene level analysis)
bull How can I use mouse ENCODE data13 in my analyses Feng Yue13 Ross Hardison13 Venkat Malladi
bull Analyzing ChIP-shy‐seq data13 Alon Goren Anshul Kundaje bull Basic introducRon to accessing ENCODERoadmap Epigenomics
data13 Anshul Kundaje Jiang Zhu Eurie Hong ENCODEEpigenomics Roadmap Workshop ASHG 2013
