SYDH TFBS Track Settings
 
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard   (ENC TF Binding)

This track is part of a parent called 'ENC TF Binding'. To show other tracks of this parent, go to the ENC TF Binding configuration page.

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Cell Line
GM12878 (Tier 1)
H1-hESC (Tier 1)
K562 (Tier 1)
A549 (Tier 2)
HeLa-S3 (Tier 2)
HepG2 (Tier 2)
HUVEC (Tier 2)
IMR90 (Tier 2)
MCF-7 (Tier 2)
SK-N-SH (Tier 2)
GM08714
GM10847
GM12891
GM12892
GM15510
GM18505
GM18526
GM18951
GM19099
GM19193
HCT-116
HEK293
HEK293-T-REx
MCF10A-Er-Src
NB4
NT2-D1
PANC-1
PBDE
PBDEFetal
Raji
SH-SY5Y
U2OS
Cell Line
All 
Factor































Factor
AP-2α   AP-2α
AP-2γ   AP-2γ
ARID3A (NB100-279)   ARID3A (NB100-279)
ARID3A (SC-8821)   ARID3A (SC-8821)
ATF1 (06-325)   ATF1 (06-325)
ATF3   ATF3
Bach1 (SC-14700)   Bach1 (SC-14700)
BAF155   BAF155
BAF170   BAF170
BDP1   BDP1
BHLHE40 (SC-101023)   BHLHE40 (SC-101023)
BHLHE40 (NB100-1800)   BHLHE40 (NB100-1800)
BRCA1 (A300-000A)   BRCA1 (A300-000A)
BRF1   BRF1
BRF2   BRF2
BRG1   BRG1
CCNT2   CCNT2
CDP (SC-6327)   CDP (SC-6327)
CEBPB   CEBPB
CEBPZ   CEBPZ
c-FOS   c-FOS
CHD1 (A301-218A)   CHD1 (A301-218A)
CHD1 (NB100-60411)   CHD1 (NB100-60411)
CHD2 (AB68301)   CHD2 (AB68301)
c-Jun   c-Jun
c-Myc   c-Myc
COREST (ab24166)   COREST (ab24166)
COREST (SC-30189)   COREST (SC-30189)
CtBP2   CtBP2
CTCF (SC-15914)   CTCF (SC-15914)
E2F1   E2F1
E2F4   E2F4
E2F6   E2F6
EBF1 (SC-137065)   EBF1 (SC-137065)
ELK1 (1277-1)   ELK1 (1277-1)
ELK4   ELK4
ERRA   ERRA
GATA1   GATA1
GATA1 (SC-266)   GATA1 (SC-266)
GATA2   GATA2
GATA3 (SC-268)   GATA3 (SC-268)
GATA3 (SC-269)   GATA3 (SC-269)
GCN5   GCN5
GRp20   GRp20
GTF2B   GTF2B
GTF2F1 (AB28179)   GTF2F1 (AB28179)
HA-E2F1   HA-E2F1
HCFC1 (NB100-68209)   HCFC1 (NB100-68209)
HMGN3   HMGN3
HNF4A   HNF4A
HSF1   HSF1
IKZF1 (IkN) (UCLA)   IKZF1 (IkN) (UCLA)
INI1   INI1
IRF1   IRF1
IRF3   IRF3
JunD   JunD
KAP1   KAP1
MafF (M8194)   MafF (M8194)
MafK (ab50322)   MafK (ab50322)
MafK (SC477)   MafK (SC477)
Max   Max
MAZ (ab85725)   MAZ (ab85725)
Mxi1 (AF4185)   Mxi1 (AF4185)
NF-E2   NF-E2
NF-E2 (SC-22827)   NF-E2 (SC-22827)
NELFe   NELFe
NFKB   NFKB
NF-YA   NF-YA
NF-YB   NF-YB
Nrf1   Nrf1
p300   p300
p300 (SC-48343)   p300 (SC-48343)
p300 (SC-584)   p300 (SC-584)
PGC1A   PGC1A
Pol2   Pol2
Pol2(phosphoS2)   Pol2(phosphoS2)
POL3   POL3
PRDM1 (9115)   PRDM1 (9115)
Rad21   Rad21
RFX5 (200-401-194)   RFX5 (200-401-194)
RPC155   RPC155
SETDB1   SETDB1
SIN3A (NB600-1263)   SIN3A (NB600-1263)
SIRT6   SIRT6
SMC3 (ab9263)   SMC3 (ab9263)
SPT20   SPT20
SREBP1   SREBP1
SREBP2   SREBP2
STAT1   STAT1
STAT2   STAT2
STAT3   STAT3
SUZ12   SUZ12
TAL1 (SC-12984)   TAL1 (SC-12984)
TBLR1 (ab24550)   TBLR1 (ab24550)
TBLR1 (NB600-270)   TBLR1 (NB600-270)
TBP   TBP
TCF7L2   TCF7L2
TCF7L2 C9B9 (2565)   TCF7L2 C9B9 (2565)
TFIIIC-110   TFIIIC-110
TR4   TR4
UBF (SC-13125)   UBF (SC-13125)
UBTF (SAB1404509)   UBTF (SAB1404509)
USF2   USF2
WHIP   WHIP
XRCC4   XRCC4
YY1   YY1
ZC3H11A (NB100-74650)   ZC3H11A (NB100-74650)
ZKSCAN1 (HPA006672)   ZKSCAN1 (HPA006672)
ZNF143 (16618-1-AP)   ZNF143 (16618-1-AP)
ZNF217   ZNF217
ZNF263   ZNF263
ZNF274   ZNF274
ZNF274 (M01)   ZNF274 (M01)
ZNF384 (HPA004051)   ZNF384 (HPA004051)
ZNF-MIZD-CP1 (ab65767)   ZNF-MIZD-CP1 (ab65767)
ZZZ3   ZZZ3
Input (Harvard)   Input (Harvard)
Input (IgG-goat)   Input (IgG-goat)
Input (IgG-mus)   Input (IgG-mus)
Input (IgG-rab)   Input (IgG-rab)
Input (Large Fragment)   Input (Large Fragment)
Input (MNase)   Input (MNase)
Input (Naked DNA)   Input (Naked DNA)
Input (Standard)   Input (Standard)
Input (UC Davis)   Input (UC Davis)
Factor































Factor
 All
Cell Line
GM12878 (Tier 1)
H1-hESC (Tier 1)
K562 (Tier 1)
A549 (Tier 2)
HeLa-S3 (Tier 2)
HepG2 (Tier 2)
HUVEC (Tier 2)
IMR90 (Tier 2)
MCF-7 (Tier 2)
SK-N-SH (Tier 2)
GM08714
GM10847
GM12891
GM12892
GM15510
GM18505
GM18526
GM18951
GM19099
GM19193
HCT-116
HEK293
HEK293-T-REx
MCF10A-Er-Src
NB4
NT2-D1
PANC-1
PBDE
PBDEFetal
Raji
SH-SY5Y
U2OS
Cell Line
All 
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hide
 GM12878  CHD2 (AB68301)  IgG-mus      Peaks  GM12878 CHD2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH    schema   2011-10-18 
 
hide
 GM12878  CHD2 (AB68301)  IgG-mus      Signal  GM12878 CHD2 IgG-mus ChIP-seq Signal from ENCODE/SYDH    schema   2011-10-18 
 
hide
 GM12878  Pol2  IgG-mus      Peaks  GM12878 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 GM12878  Pol2  IgG-mus      Signal  GM12878 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH    schema   2011-09-01 
 
hide
 GM12878  Pol2  Standard      Peaks  GM12878 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 GM12878  Pol2  Standard      Signal  GM12878 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH    schema   2011-09-01 
 
hide
 GM12878  Rad21  IgG-rab      Peaks  GM12878 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 GM12878  Rad21  IgG-rab      Signal  GM12878 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH    schema   2011-09-01 
 
hide
 GM12878  TBP  IgG-mus      Peaks  GM12878 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH    schema   2011-03-11 
 
hide
 GM12878  TBP  IgG-mus      Signal  GM12878 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH    schema   2011-09-06 
 
hide
 GM12878  ZNF274  Standard      Peaks  GM12878 ZNF274 Standard ChIP-seq Peaks from ENCODE/SYDH    schema   2011-02-20 
 
hide
 GM12878  ZNF274  Standard      Signal  GM12878 ZNF274 Standard ChIP-seq Signal from ENCODE/SYDH    schema   2011-02-20 
 
hide
 K562  CHD2 (AB68301)  IgG-rab      Peaks  K562 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH    schema   2011-07-20 
 
hide
 K562  CHD2 (AB68301)  IgG-rab      Signal  K562 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH    schema   2011-07-20 
 
hide
 K562  Pol2  IgG-mus      Peaks  K562 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  IgG-mus      Signal  K562 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Pol2  Standard  IFNα 30 min  Peaks  K562 Pol2 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  Standard  IFNα 30 min  Signal  K562 Pol2 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Pol2  Standard  IFNα 6 hr  Peaks  K562 Pol2 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  Standard  IFNα 6 hr  Signal  K562 Pol2 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Pol2  Standard  IFNγ 30 min  Peaks  K562 Pol2 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  Standard  IFNγ 30 min  Signal  K562 Pol2 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Pol2  Standard  IFNγ 6 hr  Peaks  K562 Pol2 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  Standard  IFNγ 6 hr  Signal  K562 Pol2 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Pol2  Standard      Peaks  K562 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Pol2  Standard      Signal  K562 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  Rad21  Standard      Peaks  K562 Rad21 Standard ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  Rad21  Standard      Signal  K562 Rad21 Standard ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
 
hide
 K562  TBP  IgG-mus      Peaks  K562 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH    schema   2011-07-20 
 
hide
 K562  TBP  IgG-mus      Signal  K562 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH    schema   2011-07-20 
 
hide
 K562  ZNF274  UC Davis      Peaks  K562 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH    schema   2012-03-03 
 
hide
 K562  ZNF274  UC Davis      Signal  K562 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH    schema   2011-04-08 
     Restriction Policy
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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 (normalized data from pooled replicates). ENCODE Peaks tables contain fields for statistical significance, including the minimum false discovery rate (FDR) threshold at which the test may be called significant (qValue).
Signal
Density graph (wiggle) of signal enrichment based on processed data.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

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 bp) 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 less than or equal to 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 less than or equal to 0.05 are considered to be significantly enriched compared to the input DNA control.

Release Notes

This is Release 3 (August 2012). This release adds in 37 new experiments including 1 new cell line and 7 new antibodies.

Credits

These data were generated and analyzed by the labs of Michael Snyder at Stanford University; Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at University of Southern California; and Kevin Struhl at Harvard.

Contact: Philip Cayting.

References

Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem. 2011 Apr 8;286(14):11985-96.

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.

Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May;31(9):1833-47.

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.

Publications

Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan;32(1):226-39.

Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011 Nov 4;44(3):410-23.

Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6.

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.