Transcription Factor ChIP-seq Clusters (161 factors) from ENCODE with Factorbook Motifs (CTCF)
  Factorbook Link: CTCF
Factor: CTCF
Cluster Score (out of 1000): 581
Position: chr17:57863682-57864137
Band: 17q23.1
Genomic Size: 456
View DNA for this feature (hg19/Human)

Assays for CTCF in Cluster
 
#signalabrcellTypefactorantibodytreatmentlabmore info
1128.00A A549 CTCF CTCF_(SC-5916) DEX_100nM HudsonAlpha  metadata
2208.00a AG09319 CTCF CTCF None UW  metadata
3267.00a AG10803 CTCF CTCF None UW  metadata
4555.00d Dnd41 CTCF CTCF None Broad  metadata
5102.00g GM12865 CTCF CTCF None UW  metadata
6126.00g GM12872 CTCF CTCF None UW  metadata
7143.00G GM12878 CTCF CTCF None Broad  metadata
8335.00G GM12878 CTCF CTCF_(SC-15914) None Stanford  metadata
9141.00G GM12878 CTCF CTCF None UT-A  metadata
10125.00h HCM CTCF CTCF None UW  metadata
11137.00h HCPEpiC CTCF CTCF None UW  metadata
12112.00L HepG2 CTCF CTCF None UW  metadata
13128.00h HMEC CTCF CTCF None UW  metadata
14198.00h HMF CTCF CTCF None UW  metadata
15186.00h HPAF CTCF CTCF None UW  metadata
16218.00h HSMM CTCF CTCF None Broad  metadata
17113.00I IMR90 CTCF CTCF_(SC-15914) None Stanford  metadata
18226.00K K562 CTCF CTCF_(SC-15914) None Stanford  metadata
19252.00M MCF-7 CTCF CTCF estrogen UT-A  metadata
20176.00M MCF-7 CTCF CTCF None UW  metadata
21581.00M MCF-7 CTCF CTCF vehicle UT-A  metadata
22162.00n NHDF-Ad CTCF CTCF None Broad  metadata
23115.00n NHDF-neo CTCF CTCF None UW  metadata
24206.00n NHEK CTCF CTCF None Broad  metadata
25235.00o Osteobl CTCF CTCF None Broad  metadata
26118.00r RPTEC CTCF CTCF None UW  metadata

+  Assays for CTCF Without Hits in Cluster

+  Cell Abbreviations

Canonical Motif in Cluster
  Motif Name: CTCF-ext
Motif Score: 0.75
Motif Position: chr17:57863746-57863760
Motif Strand: -
Motif display help
TAGGCAACTGCAACCthis occurrence
.g.GgaAcTGCAgccmotif consensus
A 0.25 0.13 0.21 0.14 0.14 0.44 0.86 0.02 0.05 0.03 0.00 0.85 0.06 0.08 0.21
C 0.15 0.20 0.13 0.01 0.10 0.30 0.02 0.65 0.00 0.00 1.00 0.04 0.11 0.48 0.45
G 0.30 0.47 0.37 0.78 0.72 0.07 0.09 0.09 0.01 0.97 0.00 0.03 0.70 0.38 0.15
T 0.30 0.19 0.30 0.07 0.05 0.19 0.02 0.24 0.94 0.00 0.00 0.07 0.12 0.07 0.19
Metadata:
Experiment (Assay) type:Integ Cluster
tableName:wgEncodeRegTfbsClusteredV3
File Name for downloading:wgEncodeRegTfbsClusteredV3.bed.gz
View table schema

Go to Txn Factor ChIP track controls

Source data version: ENCODE Mar 2012 Freeze
Data last updated at UCSC: 2019-01-10

Description

This track shows regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project, together with DNA binding motifs identified within these regions by the ENCODE Factorbook repository.

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 TFBS ChIP-seq data were processed using the computational pipeline developed by the ENCODE Analysis Working Group to generate uniform peaks of TF binding. Peaks for 161 transcription factors in 91 cell types are combined here into clusters to produce a summary display showing occupancy regions for each factor and motif sites within the regions when identified. Additional views of the underlying ChIP-seq data and documentation on the methods used to generate it are available from the ENCODE Uniform TFBS track.

Display Conventions

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. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. (NOTE: motif highlights are shown only in browser windows of size 50,000 bp or less, and their display can be suppressed by unchecking the highlight motifs box on the track configuration page). Arrows on the highlight designate the matching strand of the motif.

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 identified for intensive study - Tier 1 and Tier 2 - while those starting with lowercase letters designate Tier 3 cell lines.

Click on a peak cluster to see more information about the TF/cell assays contributing to the cluster, the cell line abbreviation table, and details about the highest scoring canonical motif in the cluster.

Methods

Peaks of transcription factor occupancy from uniform processing of ENCODE ChIP-seq data by the ENCODE Analysis Working Group were filtered to exclude datasets that did not pass the integrated quality metric (see "Quality Control" section of Uniform TFBS) and then 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.

The Factorbook motif discovery and annotation pipeline uses the MEME-ChIP and FIMO tools from the MEME software suite in conjunction with machine learning methods and manual curation to merge discovered motifs with known motifs reported in Jaspar and TransFac. Motif identifications reported in Wang et al. 2012 (below) were supplemented in this track with more recent data (derived from newer ENCODE datasets - Jan 2011 through Mar 2012 freezes), provided by the Factorbook team. Motif identifications from all datasets were merged, with the most significant value (qvalue) reported being picked when motifs were duplicated in multiple cell lines. The scores for the selected best-scoring motif sites were then transformed to -log10.

Release Notes

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), representing all ENCODE TF ChIP-seq passing quality assessment through the ENCODE March 2012 data freeze. The peaks used to generate these clusters were called with less stringent thresholds than used during the January 2011 uniform processing shown in Release 2 of this track. The contributing datasets are displayed as individual tracks in the ENCODE Uniform TFBS track, which is available along with the primary data tracks in the ENC TF Binding Supertrack page. The clustering for V3/V4 is based on the transcription factor target, and so differs from V2 where clustering was based on antibody.

For the V3/V4 releases, a new track table format, 'factorSource' was used to represent the primary clusters table and downloads file, wgEncodeRegTfbsClusteredV3. This format consists of standard BED5 fields (see File Formats) followed by an experiment count field (expCount) and finally two fields containing comma-separated lists. The first list field (expNums) contains numeric identifiers for experiments, keyed to the wgEncodeRegTfbsClusteredInputsV3 table, which includes such information as the experiment's underlying Uniform TFBS table name, factor targeted, antibody used, cell type, treatment (if any), and laboratory source. The second list field (expScores) contains the scores for the corresponding experiments. For convenience, the file downloads directory for this track also contains a BED file, wgEncodeRegTfbsClusteredWithCellsV3, that lists each cluster with the cluster score followed by a comma-separated list of cell types.

The Factorbook motif positions that display as green boxes on the track come from an additional table called factorbookMotifPos, and are supported by additional metadata tables such as factorbookMotifCanonical that connects different terms used for the same factor (RELA <--> NFKB1), and factorbookGeneAlias that connects terms to the the link used at factorbook.org (EGR1 <--> EGR-1), and lastly a position weight matrix table, factorbookMotifPwm, used in building the graphical sequence logo for each motif on the item details page. These tables are available on our public MySQL server and as files on our download server.

Credits

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.

References

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 Release Policy

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.