Publication: Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

PubMed ID: 23203885

Citation: Wang J, Zhuang J, Iyer S, et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013;41(Database issue):D171-D176. doi:10.1093/nar/gks1221

Funding: This track shows ChIP-seq data from the Myers Lab at the HudsonAlpha Institute for Biotechnology and by the labs of Michael Snyder, Mark Gerstein, Sherman Weissman at Yale University, Peggy Farnham at the University of Southern California, Kevin Struhl at Harvard, Kevin White at the University of Chicago, and Vishy Iyer at the University of Texas, Austin. These data were processed into uniform peak calls by the ENCODE Analysis Working Group pipeline developed by Anshul Kundaje The clustering of the uniform peaks was performed by UCSC. The Factorbook motif identifications and localizations (and valuable assistance with interpretation) were provided by Jie Wang, Bong Hyun Kim and Jiali Zhuang of the Zlab (Weng Lab) at UMass Medical School

Publication: Architecture of the human regulatory network derived from ENCODE data

PubMed ID: 22955619

Citation: Gerstein MB, Kundaje A, Hariharan M, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012;489(7414):91-100. doi:10.1038/nature11245

Funding: This track shows ChIP-seq data from the Myers Lab at the HudsonAlpha Institute for Biotechnology and by the labs of Michael Snyder, Mark Gerstein, Sherman Weissman at Yale University, Peggy Farnham at the University of Southern California, Kevin Struhl at Harvard, Kevin White at the University of Chicago, and Vishy Iyer at the University of Texas, Austin. These data were processed into uniform peak calls by the ENCODE Analysis Working Group pipeline developed by Anshul Kundaje The clustering of the uniform peaks was performed by UCSC. The Factorbook motif identifications and localizations (and valuable assistance with interpretation) were provided by Jie Wang, Bong Hyun Kim and Jiali Zhuang of the Zlab (Weng Lab) at UMass Medical School

Publication: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

PubMed ID: 22955990

Citation: Wang J, Zhuang J, Iyer S, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012;22(9):1798-1812. doi:10.1101/gr.139105.112

Funding: This track shows ChIP-seq data from the Myers Lab at the HudsonAlpha Institute for Biotechnology and by the labs of Michael Snyder, Mark Gerstein, Sherman Weissman at Yale University, Peggy Farnham at the University of Southern California, Kevin Struhl at Harvard, Kevin White at the University of Chicago, and Vishy Iyer at the University of Texas, Austin. These data were processed into uniform peak calls by the ENCODE Analysis Working Group pipeline developed by Anshul Kundaje The clustering of the uniform peaks was performed by UCSC. The Factorbook motif identifications and localizations (and valuable assistance with interpretation) were provided by Jie Wang, Bong Hyun Kim and Jiali Zhuang of the Zlab (Weng Lab) at UMass Medical School