Yale TFBS Track Settings
 
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard   (All Regulation tracks)

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Peaks Configuration
Minimum Signal value: (0 to 18241)
Minimum P-Value (-log10): (0 to 300)
Minimum Q-Value (-log10): (0 to 300)
Select subtracks by cell line and factor:
 All
Cell Line
GM12878
K562
HeLa-S3
HepG2
HUVEC
GM10847
GM12891
GM12892
GM15510
GM18505
GM18526
GM18951
GM19099
GM19193
HCT-116
HEK293(b)
MCF-7
NB4
NT2-D1 (NTera2)
HeLa-S3 IFNγ 30min
HepG2 forskolin
HepG2 insulin
HepG2 pravastatin
K562 IFNα 30min
K562 IFNα 6hrs
K562 IFNγ 30min
K562 IFNγ 6hrs
Cell Line
All 
Factor


























Factor
AP-2alpha   AP-2alpha
AP-2gamma   AP-2gamma
ATF3   ATF3
BAF155 (IgG-mus)   BAF155 (IgG-mus)
BAF170 (IgG-mus)   BAF170 (IgG-mus)
BDP1   BDP1
BRF1   BRF1
BRF2   BRF2
Brg1 (IgG-mus)   Brg1 (IgG-mus)
CEBPB   CEBPB
c-Fos   c-Fos
c-Jun   c-Jun
c-Jun (IgG-rab)   c-Jun (IgG-rab)
c-Myc   c-Myc
E2F1   E2F1
E2F1 (HA-E2F1)   E2F1 (HA-E2F1)
E2F4   E2F4
E2F6   E2F6
ERRA   ERRA
GATA-1   GATA-1
GATA-2   GATA-2
GRp20   GRp20
GTF2B   GTF2B
HNF4A   HNF4A
HSF1   HSF1
Ini1 (IgG-mus)   Ini1 (IgG-mus)
JunD   JunD
JunD (IgG-rab)   JunD (IgG-rab)
Max   Max
NELFe   NELFe
NF-E2   NF-E2
NFKB   NFKB
NFKB (IgG-rab)   NFKB (IgG-rab)
NRF1 (IgG-mus)   NRF1 (IgG-mus)
PGC1A   PGC1A
Pol2   Pol2
Pol2 (IgG-mus)   Pol2 (IgG-mus)
Pol3   Pol3
Rad21   Rad21
Rad21 (IgG-rab)   Rad21 (IgG-rab)
RPC155   RPC155
SETDB1   SETDB1
SETDB1 (MNase)   SETDB1 (MNase)
SIRT6   SIRT6
SREBP1   SREBP1
SREBP2   SREBP2
STAT1   STAT1
STAT2   STAT2
SUZ12   SUZ12
TCF7L2 (TCF4)   TCF7L2 (TCF4)
TFIIIC-110   TFIIIC-110
TR4   TR4
XRCC4   XRCC4
YY1   YY1
ZNF263   ZNF263
ZNF274   ZNF274
ZZZ3   ZZZ3
Control (DNA)   Control (DNA)
Control (Fragment)   Control (Fragment)
Input (IgG-mus)   Input (IgG-mus)
Input (IgG-rab)   Input (IgG-rab)
Input (MNase)   Input (MNase)
Input (UCDavis)   Input (UCDavis)
Input (std)   Input (std)
Factor


























Factor
 All
Cell Line
GM12878
K562
HeLa-S3
HepG2
HUVEC
GM10847
GM12891
GM12892
GM15510
GM18505
GM18526
GM18951
GM19099
GM19193
HCT-116
HEK293(b)
MCF-7
NB4
NT2-D1 (NTera2)
HeLa-S3 IFNγ 30min
HepG2 forskolin
HepG2 insulin
HepG2 pravastatin
K562 IFNα 30min
K562 IFNα 6hrs
K562 IFNγ 30min
K562 IFNγ 6hrs
Cell Line
All 
List subtracks: only selected/visible    all    ()
  Cell Line↓1 Factor↓2 views↓3   Track Name↓4    Restricted Until↓5
 
hide
 GM12878  c-Fos  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (c-Fos in GM12878 cells)    schema   2009-08-25 
 
hide
 GM12878  c-Fos  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (c-Fos in GM12878 cells)    schema   2009-08-25 
 
hide
 GM12878  JunD  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (JunD in GM12878 cells)    schema   2009-11-27 
 
hide
 GM12878  JunD  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (JunD in GM12878 cells)    schema   2009-11-27 
 
hide
 GM12878  Max  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Max in GM12878 cells)    schema   2009-10-09 
 
hide
 GM12878  Max  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Max in GM12878 cells)    schema   2009-10-09 
 
hide
 GM12878  Pol2 (IgG-mus)  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Pol2/IgG-mus in GM12878 cells)    schema   2010-10-12 
 
hide
 GM12878  Pol2 (IgG-mus)  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Pol2/IgG-mus in GM12878 cells)    schema   2010-10-12 
 
hide
 GM12878  Pol3  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Pol3 in GM12878 cells)    schema   2010-02-04 
 
hide
 GM12878  Pol3  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Pol3 in GM12878 cells)    schema   2010-02-04 
 
hide
 GM12878  TR4  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (TR4 in GM12878 cells)    schema   2010-10-07 
 
hide
 GM12878  TR4  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (TR4 in GM12878 cells)    schema   2010-10-07 
 
hide
 GM12878  YY1  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (YY1 in GM12878 cells)    schema   2010-09-19 
 
hide
 GM12878  YY1  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (YY1 in GM12878 cells)    schema   2010-09-19 
 
hide
 K562  c-Fos  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (c-Fos in K562 cells)    schema   2009-08-21 
 
hide
 K562  c-Fos  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (c-Fos in K562 cells)    schema   2009-08-21 
 
hide
 K562  JunD  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (JunD in K562 cells)    schema   2009-11-27 
 
hide
 K562  JunD  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (JunD in K562 cells)    schema   2009-11-27 
 
hide
 K562  Max  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Max in K562 cells)    schema   2009-11-25 
 
hide
 K562  Max  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Max in K562 cells)    schema   2009-11-25 
 
hide
 K562  Pol2 (IgG-mus)  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Pol2/IgG-mus in K562 cells)    schema   2010-10-12 
 
hide
 K562  Pol2 (IgG-mus)  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Pol2/IgG-mus in K562 cells)    schema   2010-10-12 
 
hide
 K562  Pol3  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (Pol3 in K562 cells)    schema   2010-08-12 
 
hide
 K562  Pol3  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (Pol3 in K562 cells)    schema   2010-08-12 
 
hide
 K562  TR4  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (TR4 in K562b cells)    schema   2010-03-22 
 
hide
 K562  TR4  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (TR4 in K562b cells)    schema   2010-03-22 
 
hide
 K562  YY1  Peaks  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Peaks (YY1 in K562b cells)    schema   2010-06-03 
 
hide
 K562  YY1  Signal  ENCODE TFBS, Yale/UCD/Harvard ChIP-seq Signal (YY1 in K562b cells)    schema   2010-06-03 
     Restriction Policy
Downloads
Data version: through the ENCODE Jan 2010 Freeze

Description

This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding (Peaks).

The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views:

Peaks
Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). ENCODE Peaks tables contain fields for statistical significance, including FDR (qValue).
Signal
Density graph (wiggle) of signal enrichment based on processed data.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et al. (2007) and Rozowsky et al. (2009).

DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.

For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate <= 0.05 when comparing the number of peaks above threshold as compared the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.05 are considered to be significantly enriched compared to the input DNA control.

Expression data generated as confirmation of the TFBS data can be found in the Yale Poly-A tracks (coming soon).

Release Notes

Update to Release 4 (Feb 2012): the GM12878/NFKB (IgG-rab) experiments and files have been revoked because the incorrect raw data files were used for generation of the processed data.

This is Release 4 (June 2011) of this track, which includes 2 additional experiments and 2 experiments, K562/NF-YA and K562/NF-YB that were present in earlier releases have been removed.

A number of previously released datasets have been replaced by updated versions. The affected database tables and files include 'V3' in the name, and metadata is marked with "submittedDataVersion=V3", followed by the specific reason. The specific reason is: Includes previously missing sequence data. Previous versions of files are available for download from the FTP site

Credits

These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at UC Davis; and Kevin Struhl at Harvard.    Contact: the Gerstein lab.

References

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M et al. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14.

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.