Transcription factor binding sites from Factorbook, ATACdb, and HOMER, derived from ChIP-seq peak calls and ATAC-seq footprinting. Coverage spans cell lines, tissues, and primary cells across adult and child samples, with strong representation of blood, kidney, brain, and liver.
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://bio.liclab.net/ATACdb/
Publication: ATACdb: a comprehensive human chromatin accessibility database
Citation: Wang F, Bai X, Wang Y, et al. ATACdb: a comprehensive human chromatin accessibility database. Nucleic Acids Res. 2021;49(D1):D55-D64. doi:10.1093/nar/gkaa943
Funding: This work was supported by Natural Science Foundation for Distinguished Young Scholars of Heilongjiang Province of China [JQ2020C004]; National Natural Science Foundation of China [81572341, 61601150]; Funding for open access charge: Natural Science Foundation for Distinguished Young Scholars of Heilongjiang Province of China [JQ2020C004].
Source: https://www.cell.com/cell-reports/pdf/S2211-1247(20)31014-7.pdf
Publication: Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types
Citation: Funk CC, Casella AM, Jung S, et al. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. Cell Rep. 2020;32(7):108029. doi:10.1016/j.celrep.2020.108029
Funding: This work was supported by the BDDS Center of the NIH Big Data to Knowledge program (U54 EB020406 to N.D.P. and L.H.), the National Institute of Aging (U01 AG046139 to N.D.P.; RF1 AG057443 to N.D.P.), the National Institute for General Medical Sciences Center for Systems Biology at the Institute for Systems Biology (P50 GM07654 to L.H. and N.D.P.), and the national Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative (R24MH114788, Owen White, PI; R24MH114815, Owen White and Ronna Hertzano, PIs; the National Human Genome Research Institute (5R01HG009018 to I.F. and R.M.,); and the National Institute of Mental Health (F30 MH120910 to A.M.C.).
Source: https://www.factorbook.org/
Publication: Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Citation: Pratt HE, Andrews GR, Phalke N, et al. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Res. 2022;50(D1):D141-D149. doi:10.1093/nar/gkab1039
Funding: NIH [U24HG009446]. Funding for open access charge: NIH [U24HG009446].
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
Source: http://homer.ucsd.edu/homer/
Citation: Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576-589. doi:10.1016/j.molcel.2010.05.004
Funding: We thank Dr. Bing Ren, Dr. Michael Rehli and Dr. Constanze Bonifer for discussions and reading of the manuscript, Dr. Gary Hardiman and especially Colleen Ludka for assistance with Solexa sequencing, Rosa Luna for technical assistance, Dr. Young-Soo Kwon for suggestions and discussions and Lynn Bautista for assistance with manuscript preparation. SH was supported by an NIH postdoctoral training grant. These studies were primarily funded by NURSA consortium grant No DK62434 and further supported by NIH grants to CKG (HC088093, DK063491, CA52599), HS (P50 GM081892-01A1) and CM and a Foundation Leducq Transatlantic Network Grant to CKG. HS is an HHMI Investigator.