-This track shows regions of transcription factor binding derived from a large collection -of ChIP-seq experiments performed by the ENCODE project between February 2011 and November 2018.
--Transcription factors (TFs) are proteins that bind to DNA and interact with RNA polymerases to -regulate gene expression. Some TFs contain a DNA binding domain and can bind directly to -specific short DNA sequences ('motifs'); -others bind to DNA indirectly through interactions with TFs containing a DNA binding domain. -High-throughput antibody capture and sequencing methods (e.g. chromatin immunoprecipitation -followed by sequencing, or 'ChIP-seq') can be used to identify regions of -TF binding genome-wide. These regions are commonly called ChIP-seq peaks.
--ENCODE TF ChIP-seq data were processed using the -ENCODE Transcription Factor ChIP-seq Processing Pipeline to generate peaks of TF binding. -Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors -(340 in hg38) in 130 cell types (129 in hg38) are combined here into clusters to produce a -summary display showing occupancy regions for each factor and motif sites -within the regions when identified. - - -
- --A gray box encloses each peak cluster of transcription factor occupancy, with the -darkness of the box being proportional to the maximum signal strength observed in any cell line -contributing to the cluster. The HGNC gene name for the transcription factor is shown -to the left of each cluster. - -
--The cell lines where signal was detected for the factor are identified by single-letter -abbreviations shown to the right of the cluster. -The darkness of each letter is proportional to the signal strength observed in the cell line. -Abbreviations starting with capital letters designate -ENCODE cell types initially identified for intensive study, -while those starting with lowercase letters designate cell lines added later in the project.
--Click on a peak cluster to see more information about the TF/cell assays contributing to the -cluster and the cell line abbreviation table. -
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-Peaks of transcription factor occupancy from ENCODE ChIP-seq datasets provided by the -ENCODE Data Analysis Center in November 2018 -were clustered using the UCSC hgBedsToBedExps tool. -Scores were assigned to peaks by multiplying the input signal values by a normalization -factor calculated as the ratio of the maximum score value (1000) to the signal value at one -standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the -effect of distributing scores up to mean plus one 1 standard deviation across the score range, -but assigning all above to the maximum score. -The cluster score is the highest score for any peak contributing to the cluster.
- - --Release 5 (2019) of this track comprises 1264 datasets (1256 in hg38), -representing work performed through the 3rd phase of ENCODE. -Release 4 (February 2014) of this track adds display of the Factorbook motifs. -Release 3 (August 2013) added 124 datasets (690 total, vs. 486 in Release 2), -
- --Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, -Alexander R et al. - -Architecture of the human regulatory network derived from ENCODE data. -Nature. 2012 Sep 6;489(7414):91-100. -PMID: 22955619 -
--Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y -et al. - -Sequence features and chromatin structure around the genomic regions bound by 119 human -transcription factors. -Genome Res. 2012 Sep;22(9):1798-812. -PMID: 22955990; PMC: PMC3431495 -
--Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et -al. - -Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE -consortium. -Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. -PMID: 23203885; PMC: PMC3531197 -
- --While primary ENCODE data was subject to a restriction period as described in the - -ENCODE data release policy, this restriction does not apply to the integrative -analysis results, and all primary data underlying this track have passed the restriction date. -The data in this track are freely available.