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Regulation Sources

Source Data

Regulatory features are generated by using a variety of genome wide epigenomic data sets. The vast majority of features are derived from ChIP-seq data available from large scale sequencing projects. The experimental data for these can be visualised via the experiment view:

Publication reference for these data can be found at the in the References for Datasets section.

To maintain a standardised peak calling methodology, we start our analyses with raw reads from each experiment. Reads (replicates are pooled) are aligned to the genome using the BWA algorithm (using default parameters). All matches to mitochondria are filtered out to avoid alignment anomalies due to similarites with autosomal regions.

Peak calling is performed using two algorithms SWEMBL (S. Wilder et al, in preparation) and CCAT (Xu et al, 2010)::

  • SWEMBL - Strict parameters (-f 150 -R 0.015) are used for most epxeriments. These were obtained using CTCF as a reference dataset.
  • SWEMBL - Less strict set (-f 150 -R 0.0025) is used for data that has a broader distribution of reads. This is generally used with DNAse1 datasets to enable a greater set of potential regulatory regions.
  • CCAT - Specialised for broad peak calling of features such as H3K36me3. Parameters were set for histone calling using a 1kb window.
The ENCODE DAC Blacklist regions are then used to filter the resultant peaks. The black list regions are also stored in the core database as 'encode_excluded' MiscFeatures.

Correspondence of Transcription Factors to ENSEMBL Genes and Jaspar Matrices (Human)

Transcription FactorEnsembl GeneJaspar Matrix(ces)
ATF3ENSG00000162772
Ap2alphaENSG00000137203 MA0003.1 PB0085.1 PB0189.1
Ap2gammaENSG00000087510 PB0087.1 PB0191.1
BAF155ENSG00000173473
BAF170ENSG00000139613
BATFENSG00000156127
BCL11AENSG00000119866
BCL3ENSG00000069399
BHLHE40ENSG00000134107 PB0007.1 PB0111.1
Bdp1ENSG00000145734
Brf1ENSG00000185024
Brf2ENSG00000104221
Brg1ENSG00000127616
CBPENSG00000005339
CTCFENSG00000102974 MA0139.1
CfosENSG00000170345 MA0099.1 MA0099.2
CjunENSG00000177606 MA0099.2
CmycENSG00000136997 MA0059.1 MA0147.1
E2F1ENSG00000101412 MA0024.1
E2F4ENSG00000205250
E2F6ENSG00000169016
EBFENSG00000164330 MA0154.1
Egr1ENSG00000120738 MA0162.1 PB0010.1 PB0114.1
FOSL2ENSG00000075426
GTF2BENSG00000137947
GabpENSG00000154727 MA0062.1 MA0062.2 PB0020.1 PB0124.1
Gata1ENSG00000102145 MA0035.1 MA0035.2 MA0140.1
Gata2ENSG00000179348 MA0036.1
HDAC1ENSG00000116478
HDAC2ENSG00000196591
HDAC3ENSG00000171720
HDAC6ENSG00000094631
HEY1ENSG00000164683
IRF4ENSG00000137265 PB0034.1 PB0138.1
Ini1ENSG00000099956
JundENSG00000130522
MaxENSG00000125952 MA0058.1 PB0043.1 PB0147.1 PL0007.1 PL0014.1
MOFENSG00000103510
NELFeENSG00000204356
NFKBENSG00000109320 MA0105.1
Nfe2ENSG00000123405
NfyaENSG00000001167 MA0060.1
NfybENSG00000120837
Nrf1ENSG00000106459
NrsfENSG00000084093 MA0138.2 MA0138.1
PCAFENSG00000114166
POU2F2ENSG00000028277 PH0144.1
PU1ENSG00000066336 MA0080.1 MA0080.2 PB0058.1 PB0162.1
Pax5ENSG00000196092 MA0014.1 MA0239.1
Pbx3ENSG00000167081
RPC155ENSG00000148606
RXRAENSG00000186350 MA0016.1 PB0057.1 PB0161.1 MA0065.2 MA0074.1 MA0115.1 MA0159.1
Rad21ENSG00000164754
SETDB1ENSG00000143379
SIX5ENSG00000177045
SP1ENSG00000185591 MA0079.1 MA0079.2
SRebp1ENSG00000072310
SRebp2ENSG00000198911
Sin3Ak20ENSG00000169375
Sirt6ENSG00000077463
SrfENSG00000112658 MA0083.1 PB0078.1
TAF1ENSG00000147133
Tip60ENSG00000172977
TFIIIC-110ENSG00000115207
Tcf12ENSG00000140262
Tr4ENSG00000177463
USF1ENSG00000158773 MA0093.1
XRCC4ENSG00000152422
Yy1ENSG00000100811 MA0095.1
ZBTB33ENSG00000177485
ZNF274ENSG00000171606
ZZZ3ENSG00000036549
Znf263ENSG00000006194
p300ENSG00000100393

Correspondence of Transcription Factors to ENSEMBL Genes and Jaspar Matrices (Mouse)

Transcription FactorEnsembl GeneJaspar Matrix(ces)
cMybENSMUSG00000019982 MA0100.1 PB0149.1 PB0045.1
CTCFENSMUSG00000005698 MA0139.1
CmycENSMUSG00000022346 MA0147.1
E2F1ENSMUSG00000027490 MA0024.1
EsrrbENSMUSG00000021255 MA0141.1
Klf4ENSMUSG00000003032 MA0039.2
MaxENSMUSG00000059436 PB0147.1 PB0043.1 PL0007.1
NanogENSMUSG00000012396
NELFeENSMUSG00000024369
nMycENSMUSG00000037169 MA0104.2
Oct4ENSMUSG00000012396
p300ENSMUSG00000055024
Rad21ENSMUSG00000022314
Smad1ENSMUSG00000031681
Sox2ENSMUSG00000074637 MA0143.1
STAT3ENSMUSG00000004040 MA0144.1
Suz12ENSMUSG00000017548
Tcfcp2l1ENSMUSG00000026380 MA0145.1
USF2ENSMUSG00000058239
ZfxENSMUSG00000079509 MA0146.1


The current release comprises of the following datasets:

Human Regulatory Build version 11

CD4
Focus SetsData typeReference
CBPChIP-Seq12
CTCFChIP-Seq3
HDAC1ChIP-Seq12
HDAC2ChIP-Seq12
HDAC3ChIP-Seq12
HDAC6ChIP-Seq12
MOFChIP-Seq12
p300ChIP-Seq12
PCAFChIP-Seq12
Tip60ChIP-Seq12
Attribute SetsData typeReference
H2AK5acChIP-Seq4
H2AK9acChIP-Seq4
H2AZChIP-Seq3
H2BK120acChIP-Seq4
H2BK12acChIP-Seq4
H2BK20acChIP-Seq4
H2BK5acChIP-Seq4
H2BK5me1ChIP-Seq3
H3K14acChIP-Seq4
H3K18acChIP-Seq4
H3K23acChIP-Seq4
H3K27acChIP-Seq4
H3K27me1ChIP-Seq3
H3K27me2ChIP-Seq3
H3K27me3ChIP-Seq3
H3K36acChIP-Seq4
H3K36me1ChIP-Seq3
H3K36me3ChIP-Seq3
H3K4acChIP-Seq4
H3K4me1ChIP-Seq3
H3K4me2ChIP-Seq3
H3K4me3ChIP-Seq3
H3K79me1ChIP-Seq3
H3K79me2ChIP-Seq3
H3K79me3ChIP-Seq3
H3K9acChIP-Seq4
H3K9me1ChIP-Seq3
H3K9me2ChIP-Seq3
H3K9me3ChIP-Seq3
H3R2me1ChIP-Seq3
H3R2me2ChIP-Seq3
H4K12acChIP-Seq4
H4K16acChIP-Seq4
H4K20me1ChIP-Seq3
H4K20me3ChIP-Seq3
H4K5acChIP-Seq4
H4K8acChIP-Seq4
H4K91acChIP-Seq4
H4R3me2ChIP-Seq3
PolIIChIP-Seq3
GM06990
Focus SetsData typeReference
CTCFChIP-Seq5
DNase1Dnase-Seq5
Attribute SetsData typeReference
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq5
H3K4me3ChIP-Seq5
GM12878
Focus SetsData typeReference
BATFChIP-Seq10
BCL11AChIP-Seq10
BCL3ChIP-Seq10
CTCFChIP-Seq7
CTCFChIP-Seq6
CfosChIP-Seq9
CmycChIP-Seq6
DNase1Dnase-Seq6
DNase1Dnase-Seq5
EBFChIP-Seq10
Egr1ChIP-Seq10
FAIREFAIRE-Seq6
GabpChIP-Seq10
IRF4ChIP-Seq10
JundChIP-Seq9
MaxChIP-Seq9
NFKBChIP-Seq9
NrsfChIP-Seq10
POU2F2ChIP-Seq10
PU1ChIP-Seq10
Pax5ChIP-Seq10
Pbx3ChIP-Seq10
Rad21ChIP-Seq9
SP1ChIP-Seq10
Sin3Ak20ChIP-Seq10
SrfChIP-Seq10
TAF1ChIP-Seq10
Tcf12ChIP-Seq10
Tr4ChIP-Seq9
USF1ChIP-Seq10
Yy1ChIP-Seq9
ZBTB33ChIP-Seq10
ZZZ3ChIP-Seq9
p300ChIP-Seq10
Attribute SetsData typeReference
H3K27acChIP-Seq7
H3K27me3ChIP-Seq7
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq5
H3K4me1ChIP-Seq7
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K9acChIP-Seq7
H4K20me1ChIP-Seq7
PolIIChIP-Seq10
PolIIChIP-Seq6
PolIIChIP-Seq9
PolIIIChIP-Seq9
H1ESC
Focus SetsData typeReference
CTCFChIP-Seq7
CmycChIP-Seq6
DNase1Dnase-Seq6
DNase1Dnase-Seq5
FAIREFAIRE-Seq6
NrsfChIP-Seq10
TAF1ChIP-Seq10
Attribute SetsData typeReference
H3K27acChIP-Seq11
H3K27me3ChIP-Seq7
H3K27me3ChIP-Seq11
H3K27me3ChIP-Seq11
H3K27me3ChIP-Seq11
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq11
H3K36me3ChIP-Seq11
H3K36me3ChIP-Seq11
H3K4me1ChIP-Seq7
H3K4me1ChIP-Seq11
H3K4me1ChIP-Seq11
H3K4me1ChIP-Seq11
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K4me3ChIP-Seq11
H3K4me3ChIP-Seq11
H3K4me3ChIP-Seq11
H3K9acChIP-Seq7
H3K9acChIP-Seq11
H3K9acChIP-Seq11
H3K9acChIP-Seq11
H3K9me3ChIP-Seq11
H3K9me3ChIP-Seq11
H3K9me3ChIP-Seq11
H4K20me1ChIP-Seq7
PolIIChIP-Seq10
PolIIChIP-Seq6
HUVEC
Focus SetsData typeReference
CTCFChIP-Seq7
CTCFChIP-Seq6
CTCFChIP-Seq5
CjunChIP-Seq9
CmycChIP-Seq6
DNase1Dnase-Seq6
DNase1Dnase-Seq5
FAIREFAIRE-Seq6
MaxChIP-Seq9
Attribute SetsData typeReference
H3K27acChIP-Seq7
H3K27me3ChIP-Seq7
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq5
H3K4me1ChIP-Seq7
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K4me3ChIP-Seq5
H3K9acChIP-Seq7
H3K9me1ChIP-Seq7
H4K20me1ChIP-Seq7
PolIIChIP-Seq7
PolIIChIP-Seq6
PolIIChIP-Seq9
HeLa
Focus SetsData typeReference
Ap2alphaChIP-Seq9
Ap2gammaChIP-Seq9
BAF155ChIP-Seq9
BAF170ChIP-Seq9
Bdp1ChIP-Seq9
Brf1ChIP-Seq9
Brf2ChIP-Seq9
Brg1ChIP-Seq9
CTCFChIP-Seq6
CTCFChIP-Seq5
CfosChIP-Seq9
CjunChIP-Seq9
CmycChIP-Seq6
CmycChIP-Seq9
DNase1Dnase-Seq6
DNase1Dnase-Seq5
E2F1ChIP-Seq9
E2F4ChIP-Seq9
E2F6ChIP-Seq9
FAIREFAIRE-Seq6
GabpChIP-Seq10
Ini1ChIP-Seq9
JundChIP-Seq9
MaxChIP-Seq9
Nrf1ChIP-Seq9
RPC155ChIP-Seq9
TAF1ChIP-Seq10
TFIIIC-110ChIP-Seq9
Tr4ChIP-Seq9
Attribute SetsData typeReference
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq5
H3K4me3ChIP-Seq5
PolIIChIP-Seq10
PolIIChIP-Seq6
PolIIChIP-Seq9
HepG2
Focus SetsData typeReference
BHLHE40ChIP-Seq10
CTCFChIP-Seq7
CTCFChIP-Seq6
CTCFChIP-Seq5
CmycChIP-Seq6
DNase1Dnase-Seq6
DNase1Dnase-Seq5
FAIREFAIRE-Seq6
FOSL2ChIP-Seq10
GabpChIP-Seq10
HEY1ChIP-Seq10
JundChIP-Seq10
RXRAChIP-Seq10
SRebp1ChIP-Seq9
SRebp2ChIP-Seq9
Sin3Ak20ChIP-Seq10
USF1ChIP-Seq10
ZBTB33ChIP-Seq10
p300ChIP-Seq10
Attribute SetsData typeReference
H3K27acChIP-Seq7
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq5
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K4me3ChIP-Seq5
H3K9acChIP-Seq7
H4K20me1ChIP-Seq7
PolIIChIP-Seq6
PolIIChIP-Seq9
IMR90
Focus SetsData typeReference
DNase1Dnase-Seq11
Attribute SetsData typeReference
H2AK5acChIP-Seq11
H2BK120acChIP-Seq11
H2BK12acChIP-Seq11
H2BK15acChIP-Seq11
H2BK20acChIP-Seq11
H3K14acChIP-Seq11
H3K18acChIP-Seq11
H3K23acChIP-Seq11
H3K27acChIP-Seq11
H3K27me3ChIP-Seq11
H3K36me3ChIP-Seq11
H3K4acChIP-Seq11
H3K4me1ChIP-Seq11
H3K4me2ChIP-Seq11
H3K4me3ChIP-Seq11
H3K56acChIP-Seq11
H3K79me1ChIP-Seq11
H3K79me2ChIP-Seq11
H3K9acChIP-Seq11
H3K9me3ChIP-Seq11
H4K20me1ChIP-Seq11
H4K5acChIP-Seq11
H4K8acChIP-Seq11
H4K91acChIP-Seq11
K562
Focus SetsData typeReference
ATF3ChIP-Seq9
Bdp1ChIP-Seq9
Brf1ChIP-Seq9
Brf2ChIP-Seq9
Brg1ChIP-Seq9
CTCFChIP-Seq7
CTCFChIP-Seq6
CTCFChIP-Seq5
CfosChIP-Seq9
CjunChIP-Seq9
CmycChIP-Seq6
CmycChIP-Seq9
DNase1Dnase-Seq6
DNase1Dnase-Seq5
Egr1ChIP-Seq10
FAIREFAIRE-Seq6
GTF2BChIP-Seq9
GabpChIP-Seq10
HEY1ChIP-Seq10
Ini1ChIP-Seq9
JundChIP-Seq9
MaxChIP-Seq9
NELFeChIP-Seq9
Nfe2ChIP-Seq9
NfyaChIP-Seq9
NfybChIP-Seq9
NrsfChIP-Seq10
PU1ChIP-Seq10
Rad21ChIP-Seq9
SIX5ChIP-Seq10
SP1ChIP-Seq10
Sin3Ak20ChIP-Seq10
Sirt6ChIP-Seq9
SrfChIP-Seq10
TAF1ChIP-Seq10
TFIIIC-110ChIP-Seq9
USF1ChIP-Seq10
XRCC4ChIP-Seq9
Attribute SetsData typeReference
H3K27acChIP-Seq7
H3K27me3ChIP-Seq7
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq5
H3K4me1ChIP-Seq7
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K4me3ChIP-Seq5
H3K9acChIP-Seq7
H3K9me1ChIP-Seq7
H4K20me1ChIP-Seq7
PolIIChIP-Seq7
PolIIChIP-Seq10
PolIIChIP-Seq6
PolIIChIP-Seq9
PolIIIChIP-Seq9
Znf263ChIP-Seq9
K562b (no Regulatory Features built, but data is available).
E2F4ChIP-Seq9
E2F6ChIP-Seq9
Gata1ChIP-Seq9
Gata2ChIP-Seq9
SETDB1ChIP-Seq9
Tr4ChIP-Seq9
Yy1ChIP-Seq9
ZNF274ChIP-Seq9
Znf263ChIP-Seq9
NHEK
Focus SetsData typeReference
CTCFChIP-Seq7
CTCFChIP-Seq6
CTCFChIP-Seq5
DNase1Dnase-Seq6
DNase1Dnase-Seq5
FAIREFAIRE-Seq6
Attribute SetsData typeReference
H3K27acChIP-Seq7
H3K27me3ChIP-Seq7
H3K27me3ChIP-Seq5
H3K36me3ChIP-Seq7
H3K36me3ChIP-Seq5
H3K4me1ChIP-Seq7
H3K4me2ChIP-Seq7
H3K4me3ChIP-Seq7
H3K4me3ChIP-Seq5
H3K9acChIP-Seq7
H3K9me1ChIP-Seq7
H4K20me1ChIP-Seq7
PolIIChIP-Seq7

Mouse Regulatory Build version 7

ES
Focus SetsData typeReference
DNase1Dnase-Seq13
CTCFChIP-Seq14
CmycChIP-Seq14
E2F1ChIP-Seq14
EsrrbChIP-Seq14
Klf4ChIP-Seq14
NanogChIP-Seq14
Oct4ChIP-Seq14
STAT3ChIP-Seq14
Smad1ChIP-Seq14
Sox2ChIP-Seq14
Suz12ChIP-Seq14
Tcfcp2I1ChIP-Seq14
ZfxChIP-Seq14
nMycChIP-Seq14
p300ChIP-Seq14
Attribute SetsData typeReference
H3ChIP-Seq15
H3K4me3ChIP-Seq15
H3K9me3ChIP-Seq15
H3K27me3ChIP-Seq15
H3K36me3ChIP-Seq15
H4K20me3ChIP-Seq15
PolIIChIP-Seq15
ES Hybrid
Attribute SetsData typeReference
H3K36me3ChIP-Seq15
H3K4me3ChIP-Seq15
H3K9me3ChIP-Seq15
MEF
Attribute SetsData typeReference
H3K27me3ChIP-Seq15
H3K36me3ChIP-Seq15
H3K4me3ChIP-Seq15
H3K9me3ChIP-Seq15
MEL
Focus SetsData typeReference
DNase1Dnase-Seq16
cMybChIP-Seq17
CTCFChIP-Seq17
MaxChIP-Seq17
NELFeChIP-Seq17
p300ChIP-Seq17
Rad21ChIP-Seq17
USF2ChIP-Seq17
NPC
Attribute SetsData typeReference
H3K27me3ChIP-Seq15
H3K36me3ChIP-Seq15
H3K4me3ChIP-Seq15
H3K9me3ChIP-Seq15

References for Datasets

1. Genome-wide identification of DNaseI hypersensitive sites was performed by Greg Crawford and Terry Furey (Duke University) using a whole genome DNase-sequencing protocol (Crawford et al., Genome Research 2006).
DNase-sequencing was performed using the Illumina (Solexa) sequencing by synthesis method from a DNase treated library generated from the GM06990 cell line (Crawford and Furey, unpublished).

2. Kim, T.H.; Abdullaev, Z.K.; Smith, A.D.; Ching, K.A.; Loukinov, D.I.; Green, R.D.; Zhang, M.Q.; Lobanenkov, V.V. & Ren, B.
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome.
Cell, 2007 , 128 , 1231-1245

3. A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, (2007). High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837. PMID: 17512414

4. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008 Jul;40(7):897-903. Epub 2008 Jun 15. PMID: 18552846

5. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. These data were generated by the UW ENCODE group. More information here and here

6. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. These data and annotations were created by a collaboration of multiple institutions. More information here

7. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School. More information here

8. Raha D, Wang Z, Moqtaderi Z, Wu L et al. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci USA 2010 Feb 23;107(8):3639-44. PMID: 20139302

9. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. 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. More information here

10. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. These data were provided by the Myers Lab at the HudsonAlpha Institute for Biotechnology. More information here

11. This data was produced as part of the Epigenomics Roadmap and is used in accordance to their data release policy. More information in here: http://nihroadmap.nih.gov/epigenomics/

12. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 2009 Sep 4;138(5):1019-31. PMID: 18555785

13. Dnase1-sequencing was produced as a collaboration between Ensembl, David Adams (Wellcome Trust Sanger Institute), and Greg Crawford (Duke University).

14. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008 Jun 13;133(6):1106-17. PMID: 18555785

15. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 2;448(7153):548-9. PMID: 17603471

16. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. These data were generated by the UW ENCODE group. More information here

17. This data was produced as part of the ENCODE project and is used in accordance to their data release policy. These data were generated and analyzed by the labs of Michael Snyder at Stanford University and Sherman Weissman at Yale University. More information here