Transcription factor ChIP-seq peaks from ENCODE, spanning cell lines, tissues, and stem cells. Coverage is extensive across adult, child, and embryonic samples, with strong representation of blood, liver, lung, kidney, and brain.
Data in this track hub were uniformly downloaded, processed, and harmonized by FILER2. Raw files were obtained from each source repository, converted to BED/bigBed format, lifted to the target genome assembly where necessary, and annotated with standardized metadata including cell type, tissue category, and assay type.
Source: https://www.encodeproject.org
Publication: An integrated encyclopedia of DNA elements in the human genome
Citation: ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247
Funding: The Consortium is funded by grants from the NHGRI as follows: Production Grants: U54HG004570 (Bernstein); U01HG004695 (Birney); U54HG004563 (Crawford); U54HG004557 (Gingeras); U54HG004555 (Hubbard); U41HG004568 (Kent); U54HG004576 (Myers); U54HG004558 (Snyder); U54HG004592 (Stamatoyannopoulos). Pilot Grants: R01HG003143 (Dekker); RC2HG005591 and R01HG003700 (Giddings); R01HG004456-03 (Ruan); U01HG004571 (Tenenbaum); U01HG004561 (Weng); RC2HG005679 (White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541, U01HG004561, RC2HG005679 and R01HG003988 (PI: Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (Elnitski, ZIAHG200323; Margulies, ZIAHG200341). Research in the Pennachio lab was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
Publication: Data navigation on the ENCODE portal
Citation: Kagda MS, Lam B, Litton C, et al. Data navigation on the ENCODE portal. Nat Commun. 2025;16(1):9592. Published 2025 Oct 30. doi:10.1038/s41467-025-64343-9
Funding: All the figures in the manuscript are prepared using the free academic licence version of Tableau Desktop 2023.1. The authors would like to thank Salesforce for providing us with a free academic version. In addition, we would like to thank all the past and present members of the ENCODE and affiliated consortia. National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Publication: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Citation: Luo Y, Hitz BC, Gabdank I, et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020;48(D1):D882-D889. doi:10.1093/nar/gkz1062
Funding: National Human Genome Research Institute, National Institutes of Health [U24 HG009397]. The content is solely theresponsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. The funders had no role in design, data processing, implementation, decision to publish, or preparation of the manuscript. Funding for open access charge: National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Source: http://www.roadmapepigenomics.org/
Publication: Integrative analysis of 111 reference human epigenomes
Citation: Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317-330. doi:10.1038/nature14248
Funding: This work was supported by the NIH Common Fund as part of the NIH Roadmap Epigenomics Program through U01ES017155 (BB/AM), U01ES017154 (JC/MM), U01ES017166 (BR), U01ES017156 (JS), U01DA025956 (AM/AB), and by NHGRI through RC1HG005334, R01HG004037 (MK), RO1NS078839 (L-HT). This work was also supported by NIH fellowship grants F32HL110473 and K99HL119617 (S.L.), and NSF CAREER award 1254200 (J.E.). We acknowledge program leadership by members of the NIH Epigenomics Workgroup, especially John S. Satterlee, Frederick L. Tyson, Joni Rutter, Kimberly A. McAllister, Astrid Haugen, Christine Colvis (NCATS), James Battey (NIDCD), Linda Birnbaum (NIEHS), and Nora Volkow (NIDA). We acknowledge feedback from our External Scientific Panel members Marisa Bartolomei, Stephen Baylin, Stephan Beck, Aravinda Chakravarti, Laurie Jackson-Grusby, Jason Lieb, Steve Peckman, John Quackenbush, and Steve Stice. Sample procurement was supported by grants 5R24HD000836 (IAG) for staged fetal tissues; P30AG10161, R01AG15819, R01AG17917 (DAB) and U01AG46152 (PLD, DAB) for adult brain samples.
Publication: Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
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
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
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