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Regulation Sources

Source Data
Correspondence of Transcription Factors to ENSEMBL Genes and Jaspar Matrices (Human)
Correspondence of Transcription Factors to ENSEMBL Genes and Jaspar Matrices (Mouse)
Human Regulatory Build Detailed Data
Mouse Regulatory Build Detailed Data
References for Datasets

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:

Roadmap Epigenomics(human)
ENCODE (human).
ENCODE (mouse).

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 Factor	Ensembl Gene	Jaspar Matrix(ces)
ATF3	ENSG00000162772
Ap2alpha	ENSG00000137203	MA0003.1 PB0085.1 PB0189.1
Ap2gamma	ENSG00000087510	PB0087.1 PB0191.1
BAF155	ENSG00000173473
BAF170	ENSG00000139613
BATF	ENSG00000156127
BCL11A	ENSG00000119866
BCL3	ENSG00000069399
BHLHE40	ENSG00000134107	PB0007.1 PB0111.1
Bdp1	ENSG00000145734
Brf1	ENSG00000185024
Brf2	ENSG00000104221
Brg1	ENSG00000127616
CBP	ENSG00000005339
CTCF	ENSG00000102974	MA0139.1
Cfos	ENSG00000170345	MA0099.1 MA0099.2
Cjun	ENSG00000177606	MA0099.2
Cmyc	ENSG00000136997	MA0059.1 MA0147.1
E2F1	ENSG00000101412	MA0024.1
E2F4	ENSG00000205250
E2F6	ENSG00000169016
EBF	ENSG00000164330	MA0154.1
Egr1	ENSG00000120738	MA0162.1 PB0010.1 PB0114.1
FOSL2	ENSG00000075426
GTF2B	ENSG00000137947
Gabp	ENSG00000154727	MA0062.1 MA0062.2 PB0020.1 PB0124.1
Gata1	ENSG00000102145	MA0035.1 MA0035.2 MA0140.1
Gata2	ENSG00000179348	MA0036.1
HDAC1	ENSG00000116478
HDAC2	ENSG00000196591
HDAC3	ENSG00000171720
HDAC6	ENSG00000094631
HEY1	ENSG00000164683
IRF4	ENSG00000137265	PB0034.1 PB0138.1
Ini1	ENSG00000099956
Jund	ENSG00000130522
Max	ENSG00000125952	MA0058.1 PB0043.1 PB0147.1 PL0007.1 PL0014.1
MOF	ENSG00000103510
NELFe	ENSG00000204356
NFKB	ENSG00000109320	MA0105.1
Nfe2	ENSG00000123405
Nfya	ENSG00000001167	MA0060.1
Nfyb	ENSG00000120837
Nrf1	ENSG00000106459
Nrsf	ENSG00000084093	MA0138.2 MA0138.1
PCAF	ENSG00000114166
POU2F2	ENSG00000028277	PH0144.1
PU1	ENSG00000066336	MA0080.1 MA0080.2 PB0058.1 PB0162.1
Pax5	ENSG00000196092	MA0014.1 MA0239.1
Pbx3	ENSG00000167081
RPC155	ENSG00000148606
RXRA	ENSG00000186350	MA0016.1 PB0057.1 PB0161.1 MA0065.2 MA0074.1 MA0115.1 MA0159.1
Rad21	ENSG00000164754
SETDB1	ENSG00000143379
SIX5	ENSG00000177045
SP1	ENSG00000185591	MA0079.1 MA0079.2
SRebp1	ENSG00000072310
SRebp2	ENSG00000198911
Sin3Ak20	ENSG00000169375
Sirt6	ENSG00000077463
Srf	ENSG00000112658	MA0083.1 PB0078.1
TAF1	ENSG00000147133
Tip60	ENSG00000172977
TFIIIC-110	ENSG00000115207
Tcf12	ENSG00000140262
Tr4	ENSG00000177463
USF1	ENSG00000158773	MA0093.1
XRCC4	ENSG00000152422
Yy1	ENSG00000100811	MA0095.1
ZBTB33	ENSG00000177485
ZNF274	ENSG00000171606
ZZZ3	ENSG00000036549
Znf263	ENSG00000006194
p300	ENSG00000100393

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

Transcription Factor	Ensembl Gene	Jaspar Matrix(ces)
cMyb	ENSMUSG00000019982	MA0100.1 PB0149.1 PB0045.1
CTCF	ENSMUSG00000005698	MA0139.1
Cmyc	ENSMUSG00000022346	MA0147.1
E2F1	ENSMUSG00000027490	MA0024.1
Esrrb	ENSMUSG00000021255	MA0141.1
Klf4	ENSMUSG00000003032	MA0039.2
Max	ENSMUSG00000059436	PB0147.1 PB0043.1 PL0007.1
Nanog	ENSMUSG00000012396
NELFe	ENSMUSG00000024369
nMyc	ENSMUSG00000037169	MA0104.2
Oct4	ENSMUSG00000012396
p300	ENSMUSG00000055024
Rad21	ENSMUSG00000022314
Smad1	ENSMUSG00000031681
Sox2	ENSMUSG00000074637	MA0143.1
STAT3	ENSMUSG00000004040	MA0144.1
Suz12	ENSMUSG00000017548
Tcfcp2l1	ENSMUSG00000026380	MA0145.1
USF2	ENSMUSG00000058239
Zfx	ENSMUSG00000079509	MA0146.1

The current release comprises of the following datasets:

Human Regulatory Build version 11

CD4
Focus Sets	Data type	Reference
CBP	ChIP-Seq	12
CTCF	ChIP-Seq	3
HDAC1	ChIP-Seq	12
HDAC2	ChIP-Seq	12
HDAC3	ChIP-Seq	12
HDAC6	ChIP-Seq	12
MOF	ChIP-Seq	12
p300	ChIP-Seq	12
PCAF	ChIP-Seq	12
Tip60	ChIP-Seq	12
Attribute Sets	Data type	Reference
H2AK5ac	ChIP-Seq	4
H2AK9ac	ChIP-Seq	4
H2AZ	ChIP-Seq	3
H2BK120ac	ChIP-Seq	4
H2BK12ac	ChIP-Seq	4
H2BK20ac	ChIP-Seq	4
H2BK5ac	ChIP-Seq	4
H2BK5me1	ChIP-Seq	3
H3K14ac	ChIP-Seq	4
H3K18ac	ChIP-Seq	4
H3K23ac	ChIP-Seq	4
H3K27ac	ChIP-Seq	4
H3K27me1	ChIP-Seq	3
H3K27me2	ChIP-Seq	3
H3K27me3	ChIP-Seq	3
H3K36ac	ChIP-Seq	4
H3K36me1	ChIP-Seq	3
H3K36me3	ChIP-Seq	3
H3K4ac	ChIP-Seq	4
H3K4me1	ChIP-Seq	3
H3K4me2	ChIP-Seq	3
H3K4me3	ChIP-Seq	3
H3K79me1	ChIP-Seq	3
H3K79me2	ChIP-Seq	3
H3K79me3	ChIP-Seq	3
H3K9ac	ChIP-Seq	4
H3K9me1	ChIP-Seq	3
H3K9me2	ChIP-Seq	3
H3K9me3	ChIP-Seq	3
H3R2me1	ChIP-Seq	3
H3R2me2	ChIP-Seq	3
H4K12ac	ChIP-Seq	4
H4K16ac	ChIP-Seq	4
H4K20me1	ChIP-Seq	3
H4K20me3	ChIP-Seq	3
H4K5ac	ChIP-Seq	4
H4K8ac	ChIP-Seq	4
H4K91ac	ChIP-Seq	4
H4R3me2	ChIP-Seq	3
PolII	ChIP-Seq	3
GM06990
Focus Sets	Data type	Reference
CTCF	ChIP-Seq	5
DNase1	Dnase-Seq	5
Attribute Sets	Data type	Reference
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	5
H3K4me3	ChIP-Seq	5
GM12878
Focus Sets	Data type	Reference
BATF	ChIP-Seq	10
BCL11A	ChIP-Seq	10
BCL3	ChIP-Seq	10
CTCF	ChIP-Seq	7
CTCF	ChIP-Seq	6
Cfos	ChIP-Seq	9
Cmyc	ChIP-Seq	6
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
EBF	ChIP-Seq	10
Egr1	ChIP-Seq	10
FAIRE	FAIRE-Seq	6
Gabp	ChIP-Seq	10
IRF4	ChIP-Seq	10
Jund	ChIP-Seq	9
Max	ChIP-Seq	9
NFKB	ChIP-Seq	9
Nrsf	ChIP-Seq	10
POU2F2	ChIP-Seq	10
PU1	ChIP-Seq	10
Pax5	ChIP-Seq	10
Pbx3	ChIP-Seq	10
Rad21	ChIP-Seq	9
SP1	ChIP-Seq	10
Sin3Ak20	ChIP-Seq	10
Srf	ChIP-Seq	10
TAF1	ChIP-Seq	10
Tcf12	ChIP-Seq	10
Tr4	ChIP-Seq	9
USF1	ChIP-Seq	10
Yy1	ChIP-Seq	9
ZBTB33	ChIP-Seq	10
ZZZ3	ChIP-Seq	9
p300	ChIP-Seq	10
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	7
H3K27me3	ChIP-Seq	7
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	5
H3K4me1	ChIP-Seq	7
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K9ac	ChIP-Seq	7
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	10
PolII	ChIP-Seq	6
PolII	ChIP-Seq	9
PolIII	ChIP-Seq	9
H1ESC
Focus Sets	Data type	Reference
CTCF	ChIP-Seq	7
Cmyc	ChIP-Seq	6
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
FAIRE	FAIRE-Seq	6
Nrsf	ChIP-Seq	10
TAF1	ChIP-Seq	10
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	11
H3K27me3	ChIP-Seq	7
H3K27me3	ChIP-Seq	11
H3K27me3	ChIP-Seq	11
H3K27me3	ChIP-Seq	11
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	11
H3K36me3	ChIP-Seq	11
H3K36me3	ChIP-Seq	11
H3K4me1	ChIP-Seq	7
H3K4me1	ChIP-Seq	11
H3K4me1	ChIP-Seq	11
H3K4me1	ChIP-Seq	11
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K4me3	ChIP-Seq	11
H3K4me3	ChIP-Seq	11
H3K4me3	ChIP-Seq	11
H3K9ac	ChIP-Seq	7
H3K9ac	ChIP-Seq	11
H3K9ac	ChIP-Seq	11
H3K9ac	ChIP-Seq	11
H3K9me3	ChIP-Seq	11
H3K9me3	ChIP-Seq	11
H3K9me3	ChIP-Seq	11
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	10
PolII	ChIP-Seq	6
HUVEC
Focus Sets	Data type	Reference
CTCF	ChIP-Seq	7
CTCF	ChIP-Seq	6
CTCF	ChIP-Seq	5
Cjun	ChIP-Seq	9
Cmyc	ChIP-Seq	6
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
FAIRE	FAIRE-Seq	6
Max	ChIP-Seq	9
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	7
H3K27me3	ChIP-Seq	7
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	5
H3K4me1	ChIP-Seq	7
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K4me3	ChIP-Seq	5
H3K9ac	ChIP-Seq	7
H3K9me1	ChIP-Seq	7
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	7
PolII	ChIP-Seq	6
PolII	ChIP-Seq	9
HeLa
Focus Sets	Data type	Reference
Ap2alpha	ChIP-Seq	9
Ap2gamma	ChIP-Seq	9
BAF155	ChIP-Seq	9
BAF170	ChIP-Seq	9
Bdp1	ChIP-Seq	9
Brf1	ChIP-Seq	9
Brf2	ChIP-Seq	9
Brg1	ChIP-Seq	9
CTCF	ChIP-Seq	6
CTCF	ChIP-Seq	5
Cfos	ChIP-Seq	9
Cjun	ChIP-Seq	9
Cmyc	ChIP-Seq	6
Cmyc	ChIP-Seq	9
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
E2F1	ChIP-Seq	9
E2F4	ChIP-Seq	9
E2F6	ChIP-Seq	9
FAIRE	FAIRE-Seq	6
Gabp	ChIP-Seq	10
Ini1	ChIP-Seq	9
Jund	ChIP-Seq	9
Max	ChIP-Seq	9
Nrf1	ChIP-Seq	9
RPC155	ChIP-Seq	9
TAF1	ChIP-Seq	10
TFIIIC-110	ChIP-Seq	9
Tr4	ChIP-Seq	9
Attribute Sets	Data type	Reference
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	5
H3K4me3	ChIP-Seq	5
PolII	ChIP-Seq	10
PolII	ChIP-Seq	6
PolII	ChIP-Seq	9
HepG2
Focus Sets	Data type	Reference
BHLHE40	ChIP-Seq	10
CTCF	ChIP-Seq	7
CTCF	ChIP-Seq	6
CTCF	ChIP-Seq	5
Cmyc	ChIP-Seq	6
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
FAIRE	FAIRE-Seq	6
FOSL2	ChIP-Seq	10
Gabp	ChIP-Seq	10
HEY1	ChIP-Seq	10
Jund	ChIP-Seq	10
RXRA	ChIP-Seq	10
SRebp1	ChIP-Seq	9
SRebp2	ChIP-Seq	9
Sin3Ak20	ChIP-Seq	10
USF1	ChIP-Seq	10
ZBTB33	ChIP-Seq	10
p300	ChIP-Seq	10
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	7
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	5
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K4me3	ChIP-Seq	5
H3K9ac	ChIP-Seq	7
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	6
PolII	ChIP-Seq	9
IMR90
Focus Sets	Data type	Reference
DNase1	Dnase-Seq	11
Attribute Sets	Data type	Reference
H2AK5ac	ChIP-Seq	11
H2BK120ac	ChIP-Seq	11
H2BK12ac	ChIP-Seq	11
H2BK15ac	ChIP-Seq	11
H2BK20ac	ChIP-Seq	11
H3K14ac	ChIP-Seq	11
H3K18ac	ChIP-Seq	11
H3K23ac	ChIP-Seq	11
H3K27ac	ChIP-Seq	11
H3K27me3	ChIP-Seq	11
H3K36me3	ChIP-Seq	11
H3K4ac	ChIP-Seq	11
H3K4me1	ChIP-Seq	11
H3K4me2	ChIP-Seq	11
H3K4me3	ChIP-Seq	11
H3K56ac	ChIP-Seq	11
H3K79me1	ChIP-Seq	11
H3K79me2	ChIP-Seq	11
H3K9ac	ChIP-Seq	11
H3K9me3	ChIP-Seq	11
H4K20me1	ChIP-Seq	11
H4K5ac	ChIP-Seq	11
H4K8ac	ChIP-Seq	11
H4K91ac	ChIP-Seq	11
K562
Focus Sets	Data type	Reference
ATF3	ChIP-Seq	9
Bdp1	ChIP-Seq	9
Brf1	ChIP-Seq	9
Brf2	ChIP-Seq	9
Brg1	ChIP-Seq	9
CTCF	ChIP-Seq	7
CTCF	ChIP-Seq	6
CTCF	ChIP-Seq	5
Cfos	ChIP-Seq	9
Cjun	ChIP-Seq	9
Cmyc	ChIP-Seq	6
Cmyc	ChIP-Seq	9
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
Egr1	ChIP-Seq	10
FAIRE	FAIRE-Seq	6
GTF2B	ChIP-Seq	9
Gabp	ChIP-Seq	10
HEY1	ChIP-Seq	10
Ini1	ChIP-Seq	9
Jund	ChIP-Seq	9
Max	ChIP-Seq	9
NELFe	ChIP-Seq	9
Nfe2	ChIP-Seq	9
Nfya	ChIP-Seq	9
Nfyb	ChIP-Seq	9
Nrsf	ChIP-Seq	10
PU1	ChIP-Seq	10
Rad21	ChIP-Seq	9
SIX5	ChIP-Seq	10
SP1	ChIP-Seq	10
Sin3Ak20	ChIP-Seq	10
Sirt6	ChIP-Seq	9
Srf	ChIP-Seq	10
TAF1	ChIP-Seq	10
TFIIIC-110	ChIP-Seq	9
USF1	ChIP-Seq	10
XRCC4	ChIP-Seq	9
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	7
H3K27me3	ChIP-Seq	7
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	5
H3K4me1	ChIP-Seq	7
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K4me3	ChIP-Seq	5
H3K9ac	ChIP-Seq	7
H3K9me1	ChIP-Seq	7
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	7
PolII	ChIP-Seq	10
PolII	ChIP-Seq	6
PolII	ChIP-Seq	9
PolIII	ChIP-Seq	9
Znf263	ChIP-Seq	9
K562b (no Regulatory Features built, but data is available).
E2F4	ChIP-Seq	9
E2F6	ChIP-Seq	9
Gata1	ChIP-Seq	9
Gata2	ChIP-Seq	9
SETDB1	ChIP-Seq	9
Tr4	ChIP-Seq	9
Yy1	ChIP-Seq	9
ZNF274	ChIP-Seq	9
Znf263	ChIP-Seq	9
NHEK
Focus Sets	Data type	Reference
CTCF	ChIP-Seq	7
CTCF	ChIP-Seq	6
CTCF	ChIP-Seq	5
DNase1	Dnase-Seq	6
DNase1	Dnase-Seq	5
FAIRE	FAIRE-Seq	6
Attribute Sets	Data type	Reference
H3K27ac	ChIP-Seq	7
H3K27me3	ChIP-Seq	7
H3K27me3	ChIP-Seq	5
H3K36me3	ChIP-Seq	7
H3K36me3	ChIP-Seq	5
H3K4me1	ChIP-Seq	7
H3K4me2	ChIP-Seq	7
H3K4me3	ChIP-Seq	7
H3K4me3	ChIP-Seq	5
H3K9ac	ChIP-Seq	7
H3K9me1	ChIP-Seq	7
H4K20me1	ChIP-Seq	7
PolII	ChIP-Seq	7

Mouse Regulatory Build version 7

ES
Focus Sets	Data type	Reference
DNase1	Dnase-Seq	13
CTCF	ChIP-Seq	14
Cmyc	ChIP-Seq	14
E2F1	ChIP-Seq	14
Esrrb	ChIP-Seq	14
Klf4	ChIP-Seq	14
Nanog	ChIP-Seq	14
Oct4	ChIP-Seq	14
STAT3	ChIP-Seq	14
Smad1	ChIP-Seq	14
Sox2	ChIP-Seq	14
Suz12	ChIP-Seq	14
Tcfcp2I1	ChIP-Seq	14
Zfx	ChIP-Seq	14
nMyc	ChIP-Seq	14
p300	ChIP-Seq	14
Attribute Sets	Data type	Reference
H3	ChIP-Seq	15
H3K4me3	ChIP-Seq	15
H3K9me3	ChIP-Seq	15
H3K27me3	ChIP-Seq	15
H3K36me3	ChIP-Seq	15
H4K20me3	ChIP-Seq	15
PolII	ChIP-Seq	15
ES Hybrid
Attribute Sets	Data type	Reference
H3K36me3	ChIP-Seq	15
H3K4me3	ChIP-Seq	15
H3K9me3	ChIP-Seq	15
MEF
Attribute Sets	Data type	Reference
H3K27me3	ChIP-Seq	15
H3K36me3	ChIP-Seq	15
H3K4me3	ChIP-Seq	15
H3K9me3	ChIP-Seq	15
MEL
Focus Sets	Data type	Reference
DNase1	Dnase-Seq	16
cMyb	ChIP-Seq	17
CTCF	ChIP-Seq	17
Max	ChIP-Seq	17
NELFe	ChIP-Seq	17
p300	ChIP-Seq	17
Rad21	ChIP-Seq	17
USF2	ChIP-Seq	17
NPC
Attribute Sets	Data type	Reference
H3K27me3	ChIP-Seq	15
H3K36me3	ChIP-Seq	15
H3K4me3	ChIP-Seq	15
H3K9me3	ChIP-Seq	15

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).

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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