ENCODE Regulation TF ChIP Track Settings
 
Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3

Track collection: Integrated Regulation from ENCODE

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Score range: min: (0 to 1000)
Select subtracks by cell type and factor: (help)
 All
Cell Type
22Rv1
A549
A673
AG04449
AG04450
AG09309
AG09319
AG10803
BE2C
BJ
B cell
C4-2B
CD14-positive monocyte
Caco-2
DOHH2
GM06990
GM08714
GM10266
GM12864
GM12865
GM12873
GM12874
GM12878
GM12891
GM12892
GM13977
GM20000
GM23248
GM23338
H1-hESC
H54
HCT116
HEK293
HEK293T
HFF-Myc
HL-60
HeLa-S3
HepG2
IMR-90
Ishikawa
K562
KMS-11
LNCAP
LNCaP clone FGC
Loucy
MCF-7
MCF 10A
MM.1S
NB4
NCI-H929
NT2/D1
OCI-LY1
OCI-LY3
OCI-LY7
PC-3
PC-9
PFSK-1
Panc1
Parathyroid adenoma
Peyer's patch
RWPE1
RWPE2
Raji
SH-SY5Y
SK-N-MC
SK-N-SH
SU-DHL-6
T47D
VCaP
WERI-Rb-1
WI38
adrenal gland
ascending aorta
astrocyte
astrocyte of the cerebellum
astrocyte of the spinal cord
bipolar neuron
body of pancreas
brain microvascular endothelial cell
breast epithelium
cardiac fibroblast
cardiac muscle cell
choroid plexus epithelial cell
endothelial cell of umbilical vein
epithelial cell of esophagus
epithelial cell of prostate
erythroblast
esophagus muscularis mucosa
esophagus squamous epithelium
fibroblast of lung
fibroblast of mammary gland
fibroblast of pulmonary artery
fibroblast of the aortic adventitia
fibroblast of villous mesenchyme
foreskin fibroblast
foreskin keratinocyte
gastrocnemius medialis
gastroesophageal sphincter
heart left ventricle
hepatocyte
keratinocyte
kidney epithelial cell
liver
lower leg skin
mammary epithelial cell
medulloblastoma
myotube
neural cell
neural progenitor cell
neutrophil
omental fat pad
ovary
prostate gland
retinal pigment epithelial cell
right lobe of liver
sigmoid colon
smooth muscle cell
spleen
stomach
subcutaneous adipose tissue
suprapubic skin
testis
thyroid gland
tibial artery
tibial nerve
transverse colon
upper lobe of left lung
uterus
vagina
Cell Type
All 
Factor
































































































































Factor
AFF1   AFF1
AGO1   AGO1
AGO2   AGO2
ARHGAP35   ARHGAP35
ARID1B   ARID1B
ARID2   ARID2
ARID3A   ARID3A
ARNT   ARNT
ASH1L   ASH1L
ASH2L   ASH2L
ATF2   ATF2
ATF3   ATF3
ATF4   ATF4
ATF7   ATF7
ATM   ATM
BACH1   BACH1
BATF   BATF
BCL11A   BCL11A
BCL3   BCL3
BCOR   BCOR
BHLHE40   BHLHE40
BMI1   BMI1
BRCA1   BRCA1
BRD4   BRD4
BRD9   BRD9
C11orf30   C11orf30
CBFA2T2   CBFA2T2
CBFA2T3   CBFA2T3
CBFB   CBFB
CBX1   CBX1
CBX2   CBX2
CBX3   CBX3
CBX5   CBX5
CBX8   CBX8
CC2D1A   CC2D1A
CCAR2   CCAR2
CDC5L   CDC5L
CEBPB   CEBPB
CHAMP1   CHAMP1
CHD1   CHD1
CHD4   CHD4
CHD7   CHD7
CLOCK   CLOCK
COPS2   COPS2
CREB1   CREB1
CREB3L1   CREB3L1
CREBBP   CREBBP
CREM   CREM
CTBP1   CTBP1
CTCF   CTCF
CUX1   CUX1
DACH1   DACH1
DEAF1   DEAF1
DNMT1   DNMT1
DPF2   DPF2
E2F1   E2F1
E2F4   E2F4
E2F6   E2F6
E2F7   E2F7
E2F8   E2F8
E4F1   E4F1
EBF1   EBF1
EED   EED
EGR1   EGR1
EHMT2   EHMT2
ELF1   ELF1
ELF4   ELF4
ELK1   ELK1
EP300   EP300
EP400   EP400
ESR1   ESR1
ESRRA   ESRRA
ETS1   ETS1
ETV4   ETV4
ETV6   ETV6
EWSR1   EWSR1
EZH2   EZH2
FIP1L1   FIP1L1
FOS   FOS
FOSL1   FOSL1
FOSL2   FOSL2
FOXA1   FOXA1
FOXA2   FOXA2
FOXK2   FOXK2
FOXM1   FOXM1
FOXP1   FOXP1
FUS   FUS
GABPA   GABPA
GABPB1   GABPB1
GATA1   GATA1
GATA2   GATA2
GATA3   GATA3
GATA4   GATA4
GATAD2A   GATAD2A
GATAD2B   GATAD2B
GMEB1   GMEB1
HCFC1   HCFC1
HDAC1   HDAC1
HDAC2   HDAC2
HDAC3   HDAC3
HDAC6   HDAC6
HES1   HES1
HMBOX1   HMBOX1
HNF1A   HNF1A
HNF4A   HNF4A
HNF4G   HNF4G
HNRNPH1   HNRNPH1
HNRNPK   HNRNPK
HNRNPL   HNRNPL
HNRNPLL   HNRNPLL
HNRNPUL1   HNRNPUL1
HSF1   HSF1
IKZF1   IKZF1
IKZF2   IKZF2
IRF1   IRF1
IRF2   IRF2
IRF3   IRF3
IRF4   IRF4
IRF5   IRF5
JUN   JUN
JUNB   JUNB
JUND   JUND
KAT2A   KAT2A
KAT2B   KAT2B
KAT8   KAT8
KDM1A   KDM1A
KDM4A   KDM4A
KDM4B   KDM4B
KDM5A   KDM5A
KDM5B   KDM5B
KLF16   KLF16
KLF5   KLF5
L3MBTL2   L3MBTL2
LCORL   LCORL
LEF1   LEF1
MAFF   MAFF
MAFK   MAFK
MAX   MAX
MBD2   MBD2
MCM2   MCM2
MCM3   MCM3
MCM5   MCM5
MCM7   MCM7
MEF2A   MEF2A
MEF2B   MEF2B
MEF2C   MEF2C
MEIS2   MEIS2
MGA   MGA
MIER1   MIER1
MITF   MITF
MLLT1   MLLT1
MNT   MNT
MTA1   MTA1
MTA2   MTA2
MTA3   MTA3
MXI1   MXI1
MYB   MYB
MYBL2   MYBL2
MYC   MYC
MYNN   MYNN
NANOG   NANOG
NBN   NBN
NCOA1   NCOA1
NCOA2   NCOA2
NCOA3   NCOA3
NCOA4   NCOA4
NCOA6   NCOA6
NCOR1   NCOR1
NEUROD1   NEUROD1
NFATC1   NFATC1
NFATC3   NFATC3
NFE2   NFE2
NFE2L2   NFE2L2
NFIB   NFIB
NFIC   NFIC
NFRKB   NFRKB
NFXL1   NFXL1
NFYA   NFYA
NFYB   NFYB
NR0B1   NR0B1
NR2C1   NR2C1
NR2C2   NR2C2
NR2F1   NR2F1
NR2F2   NR2F2
NR2F6   NR2F6
NR3C1   NR3C1
NRF1   NRF1
NUFIP1   NUFIP1
PAX5   PAX5
PAX8   PAX8
PBX3   PBX3
PCBP1   PCBP1
PCBP2   PCBP2
PHB2   PHB2
PHF20   PHF20
PHF21A   PHF21A
PHF8   PHF8
PKNOX1   PKNOX1
PLRG1   PLRG1
PML   PML
POLR2A   POLR2A
POLR2G   POLR2G
POU2F2   POU2F2
PRDM10   PRDM10
PRPF4   PRPF4
PTBP1   PTBP1
PYGO2   PYGO2
RAD21   RAD21
RAD51   RAD51
RB1   RB1
RBBP5   RBBP5
RBFOX2   RBFOX2
RBM14   RBM14
RBM15   RBM15
RBM17   RBM17
RBM22   RBM22
RBM25   RBM25
RBM34   RBM34
RBM39   RBM39
RCOR1   RCOR1
RELB   RELB
REST   REST
RFX1   RFX1
RFX5   RFX5
RLF   RLF
RNF2   RNF2
RUNX1   RUNX1
RUNX3   RUNX3
RXRA   RXRA
SAFB   SAFB
SAFB2   SAFB2
SAP30   SAP30
SETDB1   SETDB1
SIN3A   SIN3A
SIN3B   SIN3B
SIRT6   SIRT6
SIX4   SIX4
SIX5   SIX5
SKI   SKI
SKIL   SKIL
SMAD1   SMAD1
SMAD2   SMAD2
SMAD5   SMAD5
SMARCA4   SMARCA4
SMARCA5   SMARCA5
SMARCB1   SMARCB1
SMARCC2   SMARCC2
SMARCE1   SMARCE1
SMC3   SMC3
SNRNP70   SNRNP70
SOX13   SOX13
SOX6   SOX6
SP1   SP1
SPI1   SPI1
SREBF1   SREBF1
SREBF2   SREBF2
SRF   SRF
SRSF4   SRSF4
SRSF7   SRSF7
SRSF9   SRSF9
STAT1   STAT1
STAT2   STAT2
STAT3   STAT3
STAT5A   STAT5A
SUPT20H   SUPT20H
SUZ12   SUZ12
TAF1   TAF1
TAF15   TAF15
TAF7   TAF7
TAF9B   TAF9B
TAL1   TAL1
TBL1XR1   TBL1XR1
TBP   TBP
TBX21   TBX21
TBX3   TBX3
TCF12   TCF12
TCF7   TCF7
TCF7L2   TCF7L2
TEAD4   TEAD4
TFAP4   TFAP4
THAP1   THAP1
THRA   THRA
TRIM22   TRIM22
TRIM24   TRIM24
TRIM28   TRIM28
TRIP13   TRIP13
U2AF1   U2AF1
U2AF2   U2AF2
UBTF   UBTF
USF1   USF1
USF2   USF2
WHSC1   WHSC1
WRNIP1   WRNIP1
XRCC3   XRCC3
XRCC5   XRCC5
YY1   YY1
ZBED1   ZBED1
ZBTB1   ZBTB1
ZBTB11   ZBTB11
ZBTB2   ZBTB2
ZBTB33   ZBTB33
ZBTB40   ZBTB40
ZBTB5   ZBTB5
ZBTB7A   ZBTB7A
ZBTB7B   ZBTB7B
ZBTB8A   ZBTB8A
ZEB1   ZEB1
ZEB2   ZEB2
ZFP91   ZFP91
ZFX   ZFX
ZHX1   ZHX1
ZHX2   ZHX2
ZKSCAN1   ZKSCAN1
ZMIZ1   ZMIZ1
ZMYM3   ZMYM3
ZNF143   ZNF143
ZNF184   ZNF184
ZNF207   ZNF207
ZNF217   ZNF217
ZNF24   ZNF24
ZNF263   ZNF263
ZNF274   ZNF274
ZNF280A   ZNF280A
ZNF282   ZNF282
ZNF316   ZNF316
ZNF318   ZNF318
ZNF384   ZNF384
ZNF407   ZNF407
ZNF444   ZNF444
ZNF507   ZNF507
ZNF512B   ZNF512B
ZNF574   ZNF574
ZNF579   ZNF579
ZNF592   ZNF592
ZNF639   ZNF639
ZNF687   ZNF687
ZNF8   ZNF8
ZNF830   ZNF830
ZSCAN29   ZSCAN29
ZZZ3   ZZZ3
Factor
































































































































Factor
 All
Cell Type
22Rv1
A549
A673
AG04449
AG04450
AG09309
AG09319
AG10803
BE2C
BJ
B cell
C4-2B
CD14-positive monocyte
Caco-2
DOHH2
GM06990
GM08714
GM10266
GM12864
GM12865
GM12873
GM12874
GM12878
GM12891
GM12892
GM13977
GM20000
GM23248
GM23338
H1-hESC
H54
HCT116
HEK293
HEK293T
HFF-Myc
HL-60
HeLa-S3
HepG2
IMR-90
Ishikawa
K562
KMS-11
LNCAP
LNCaP clone FGC
Loucy
MCF-7
MCF 10A
MM.1S
NB4
NCI-H929
NT2/D1
OCI-LY1
OCI-LY3
OCI-LY7
PC-3
PC-9
PFSK-1
Panc1
Parathyroid adenoma
Peyer's patch
RWPE1
RWPE2
Raji
SH-SY5Y
SK-N-MC
SK-N-SH
SU-DHL-6
T47D
VCaP
WERI-Rb-1
WI38
adrenal gland
ascending aorta
astrocyte
astrocyte of the cerebellum
astrocyte of the spinal cord
bipolar neuron
body of pancreas
brain microvascular endothelial cell
breast epithelium
cardiac fibroblast
cardiac muscle cell
choroid plexus epithelial cell
endothelial cell of umbilical vein
epithelial cell of esophagus
epithelial cell of prostate
erythroblast
esophagus muscularis mucosa
esophagus squamous epithelium
fibroblast of lung
fibroblast of mammary gland
fibroblast of pulmonary artery
fibroblast of the aortic adventitia
fibroblast of villous mesenchyme
foreskin fibroblast
foreskin keratinocyte
gastrocnemius medialis
gastroesophageal sphincter
heart left ventricle
hepatocyte
keratinocyte
kidney epithelial cell
liver
lower leg skin
mammary epithelial cell
medulloblastoma
myotube
neural cell
neural progenitor cell
neutrophil
omental fat pad
ovary
prostate gland
retinal pigment epithelial cell
right lobe of liver
sigmoid colon
smooth muscle cell
spleen
stomach
subcutaneous adipose tissue
suprapubic skin
testis
thyroid gland
tibial artery
tibial nerve
transverse colon
upper lobe of left lung
uterus
vagina
Cell Type
All 
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  Cell Type↓1 Factor↓2   Track Name↓3  
 
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 GM12878  CTCF  Transcription Factor ChIP-seq Peaks of CTCF in GM12878 from ENCODE 3 (ENCFF356LIU)   Data format 
 
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 GM12878  RFX5  Transcription Factor ChIP-seq Peaks of RFX5 in GM12878 from ENCODE 3 (ENCFF259LNG)   Data format 
 
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 GM12878  STAT1  Transcription Factor ChIP-seq Peaks of STAT1 in GM12878 from ENCODE 3 (ENCFF323QQU)   Data format 
 
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 GM12878  TAF1  Transcription Factor ChIP-seq Peaks of TAF1 in GM12878 from ENCODE 3 (ENCFF540AAP)   Data format 
 
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 GM12878  TRIM22  Transcription Factor ChIP-seq Peaks of TRIM22 in GM12878 from ENCODE 3 (ENCFF830TFU)   Data format 
 
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 H1-hESC  CTCF  Transcription Factor ChIP-seq Peaks of CTCF in H1-hESC from ENCODE 3 (ENCFF368LWM)   Data format 
 
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 H1-hESC  REST  Transcription Factor ChIP-seq Peaks of REST in H1-hESC from ENCODE 3 (ENCFF779CWH)   Data format 
 
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 HeLa-S3  GABPA  Transcription Factor ChIP-seq Peaks of GABPA in HeLa-S3 from ENCODE 3 (ENCFF091UDB)   Data format 
 
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 HeLa-S3  MAFK  Transcription Factor ChIP-seq Peaks of MAFK in HeLa-S3 from ENCODE 3 (ENCFF328IZQ)   Data format 
 
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 HeLa-S3  TBP  Transcription Factor ChIP-seq Peaks of TBP in HeLa-S3 from ENCODE 3 (ENCFF302RQH)   Data format 
 
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 HepG2  FOXA1  Transcription Factor ChIP-seq Peaks of FOXA1 in HepG2 from ENCODE 3 (ENCFF152BOT)   Data format 
 
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 HepG2  SIN3A  Transcription Factor ChIP-seq Peaks of SIN3A in HepG2 from ENCODE 3 (ENCFF635YMI)   Data format 
 
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 HepG2  SP1  Transcription Factor ChIP-seq Peaks of SP1 in HepG2 from ENCODE 3 (ENCFF175VXL)   Data format 
 
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 K562  CTCF  Transcription Factor ChIP-seq Peaks of CTCF in K562 from ENCODE 3 (ENCFF843VHC)   Data format 
 
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 K562  GATA2  Transcription Factor ChIP-seq Peaks of GATA2 in K562 from ENCODE 3 (ENCFF173TXA)   Data format 
 
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 K562  MYC  Transcription Factor ChIP-seq Peaks of MYC in K562 from ENCODE 3 (ENCFF700TLG)   Data format 
 
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 body of pancreas  POLR2A  Transcription Factor ChIP-seq Peaks of POLR2A in body_of_pancreas from ENCODE 3 (ENCFF389ULP)   Data format 
 
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 endothelial cell of umbilical vein  FOS  Transcription Factor ChIP-seq Peaks of FOS in endothelial_cell_of_umbilical_vein from ENCODE 3 (ENCFF327GZX)   Data format 
    
Source data version: ENCODE 3 Nov 2018
Assembly: Human Dec. 2013 (GRCh38/hg38)

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.