Description
This track represents a comprehensive set of human transcription factor binding sites based on
ChIP-seq experiments generated by production groups in the ENCODE Consortium 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.
The related
Transcription Factor ChIP-seq Clusters tracks
(
hg19,
hg38)
provide summary views of this data.
Display and File Conventions and Configuration
The display for this track shows site location with the point-source of the peak marked with a
colored vertical bar and the level of enrichment at the site indicated by the darkness of the item.
The subtracks are colored by UCSC ENCODE 2 cell type color conventions on the hg19 assembly,
and by similarity of cell types in DNaseI hypersensitivity assays (as in the
DNase Signal)
track in the hg38 assembly.
The display can be filtered to higher valued items, using the
Score range: configuration item.
The score values were computed at UCSC based on signal values assigned by the ENCODE
pipeline.
The input signal values were multiplied by a normalization factor calculated as the ratio
of the maximum score value (1000) to the signal value at 1 standard deviation from the mean,
with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to
mean + 1std across the score range, but assigning all above to the maximum score.
Methods
The ChIP-seq peaks in this track were
generated by the
the ENCODE Transcription Factor ChIP-seq Processing Pipeline.
Methods documentation and full metadata for each track can be found at the
ENCODE project portal, using
The ENCODE file accession (ENCFF*) listed in the track label.
Credits
Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the
ENCODE Data Coordination Center for generating and processing the datasets used here.
Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the
ENCODE Data Analysis Center
(ZLab at UMass Medical Center) for providing the peak datasets, metadata,
and guidance developing this track. Please check the
ZLab ENCODE Public Hubs
for the most updated data.
References
ENCODE Project Consortium.
A user's guide to the encyclopedia of DNA elements (ENCODE).
PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585
ENCODE Project Consortium.
An integrated encyclopedia of DNA elements in the human genome.
Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee
BT et al.
ENCODE data at the ENCODE portal.
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32.
PMID: 26527727; PMC: PMC4702836
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
Data Use Policy
Users may freely download, analyze and publish results based on any ENCODE data without
restrictions.
Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.
Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE
production laboratory(s) that generated the datasets used, as described in
Citing ENCODE.