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[ENCODE: DNase hypersensitivity sites - Histone modifications - ChIP-Seq data]
[Genomatix ChIP-Seq data: Human - Mouse]
[Chromatin States] [Constrained Elemements]

1. ENCODE data

References:

1. DNase hypersensitivity sites

The tracks in "DNase hypersensitivity sites" show regions where the chromatin is hypersensitive to cutting by the DNase enzyme. In Genome Browser, the tracks can be loaded individually for each cell type or as a supertrack consisting of DNase hypersensitivity sites from all cell types. At the functional level hypersensitive sites often represent transcriptional active regions.

DNase hypersensitivity sites are available for the cell types listed below.

tissue cell type
blood Cd20, Cd34mobilized, Cll, Cmk, Gm06990, Gm12864, Gm12865, Gm12878, Gm12891, Gm12892, Gm18507, Gm19238, Gm19239, Gm19240, Hl60, Jurkat, K562, Monocytescd14ro01746, Nb4, Th0, Th1, Th2
blood vessel Aoaf, Aosmc, Hbmec, Hmvecdad, Hmvecdblad, Hmvecdblneo, Hmvecdlyad, Hmvecdlyneo, Hmvecdneo, Hmveclbl, Hmveclly, Hpaec, Hpaf, Huvec
bone Osteobl
brain Be2c, Gliobla, Hac, Hah, Medullo, Nha, Sknmc, Sknshra, spinal cord
breast Hmec, Hmf, Mcf7, Mcf7hypoxia, T47d
colon Caco2, Hct116
connective tissue Hvmf
embryonic stem cells Chorion, H1hesc, H7hesc, H9es, Htr8svn, Ips, Wi38, Wi38tamoxifentamoxifen
epithelium A549, Haepic, Hcpepic, Heepic, Hipepic, Hnpcepic, Hpdlf, Hrcepic, Hre, Hrpepic, Phte, Rptec, Saec
eye Hconf, Werirb1
gingival Ag09319, Hgf
heart Hcf, Hcfaa, Hcm
kidney Hrgec, urothelium
liver 8988t, Hepatocytes, Hepg2, Huh7, Stellate
lung Ag04450, Hpf, Nhlf
muscle Hsmm, Hsmmemb, Hsmmtube, Skmc
pancreas Hpde6e6e7, Panc1, Panisletd, Panislets
prostate Lncap, Lncapandrogen, Prec, Rwpe1
skin Ag04449, Ag09309, Ag10803, Bj, Fibrobl, Fibrop, Melano, Nhdfad, Nhdfneo, Nhek, Progfib, foreskin
testis Nt2d1
uterus Ishikawaestradiol, Ishikawatamoxifen, Myometr, cervix

2. Histone modification data

The tracks in "Histone modifications" show regions with modifications of the histones H3k27ac, H3K4me1-3 and H3K9ac. In Genome Browser, the tracks can be loaded individually for each cell type or as histone-specific supertracks combined of all cell types. The original ENCODE tracks have been post-processed by Genomatix. Overlapping regions have been merged and the maximum score has been assigned to the merged regions. The score represents the maximum signal strength observed in any cell type. At the functional level the histone peaks are associated with transcriptional activity.

Histone modification data is available for the cell types listed below.

tissue cell type
blood Gm12878, K562
blood vessel Huvec
breast Hmec
embryonic stem cell H1hesc
liver HepG2
lung Nhlf
muscle Hsmm
skin Nhek

3. ChIP-Seq data

The tracks in the categories "TF binding site", "Polyermase binding site" and "Other factor binding site" show ChIP-Seq peaks of more than 120 factors. The original ENCODE data has been post-processed by Genomatix. Overlapping regions of the same factor and same cell type (but different antibody or treatment) have been merged and the maximum score has been assigned to the merged regions. The score represents the maximum signal strength observed in the cell types.

Transcription factor binding data is available for the cell types listed below.

tissue cell type transcription factor
blood Dnd41 CTCF, EZH2
GM06990 CTCF
GM08714 ZNF274
GM10847 RELA
GM12801 CTCF
GM12864 CTCF
GM12865 CTCF
GM12872 CTCF
GM12873 CTCF
GM12874 CTCF
GM12875 CTCF
GM12878 ATF2, ATF3, BATF, BCL11A, BCL3, BCLAF1, BHLHE40, BRCA1, CEBPB, CHD1, CHD2, CTCF, E2F4, EBF1, EGR1, ELF1, ELK1, EP300, ETS1, EZH2, FOS, FOXM1, GABPA, IKZF1, IRF4, JUND, MAX, MAZ, MEF2A, MEF2C, MTA3, MXI1, MYC, NFATC1, NFE2, NFIC, NFYA, NFYB, NR2C2, NRF1, PAX5, PBX3, PML, POU2F2, RCOR1, RELA, REST, RFX5, RUNX3, RXRA, SIN3A, SIX5, SP1, SPI1, SRF, STAT1, STAT3, STAT5A, TAF1, TBL1XR1, TBP, TCF12, TCF3, USF1, USF2, YY1, ZBTB33, ZEB1, ZNF143, ZNF274, ZZZ3
GM12891 CTCF, PAX5, POU2F2, RELA, SPI1, TAF1, YY1
GM12892 CTCF, PAX5, RELA, TAF1, YY1
GM15510 RELA
GM18505 RELA
GM18526 RELA
GM18951 RELA
GM19099 RELA
GM19193 RELA
GM19238 CTCF
GM19239 CTCF
GM19240 CTCF
HL-60 CTCF
K562 ARID3A, ATF1, ATF3, BACH1, BCL3, BCLAF1, BDP1, BHLHE40, BRF1, BRF2, CBX3, CCNT2, CEBPB, CHD1, CHD2, CTCF, CTCFL, E2F4, E2F6, EGR1, ELF1, ELK1, EP300, ETS1, EZH2, FOS, FOSL1, GABPA, GATA1, GATA2, GTF2B, GTF2F1, GTF3C2, HDAC1, HDAC2, HDAC6, HDAC8, HMGN3, IRF1, JUN, JUNB, JUND, KDM5B, MAFF, MAFK, MAX, MAZ, MEF2A, MXI1, MYC, NELFE, NFE2, NFYA, NFYB, NR2C2, NR2F2, NRF1, PHF8, PML, RBBP5, RCOR1, REST, RFX5, SAP30, SETDB1, SIN3A, SIRT6, SIX5, SMARCA4, SMARCB1, SP1, SP2, SPI1, SRF, STAT1, STAT2, STAT5A, TAF1, TAF7, TAL1, TBL1XR1, TBP, TEAD4, THAP1, TRIM28, UBTF, USF1, USF2, YY1, ZBTB33, ZBTB7A, ZNF143, ZNF263, ZNF274
NB4 CTCF, MAX, MYC
PBDE GATA1
blood vessel AoAF CTCF
HBMEC CTCF
HPAF CTCF
HUVEC CTCF, EZH2, FOS, GATA2, JUN, MAX, MYC
bone Osteobl CTCF
U2OS SETDB1, TRIM28
brain BE2_C CTCF
Gliobla CTCF
HA-sp CTCF
HAc CTCF
NH-A CTCF, EZH2
PFSK-1 FOXP2, REST, SIN3A, TAF1
SH-SY5Y GATA2, GATA3
SK-N-MC FOXP2
SK-N-SH REST, SIN3A, TAF1
SK-N-SH_RA CTCF, EP300, USF1, YY1
U87 REST
breast HMEC CTCF, EZH2
HMF CTCF
MCF-7 CTCF, E2F1, GATA3, MYC, TCF7L2, ZNF217
MCF10A-Er-Src E2F4, FOS, MYC, STAT3
T-47D CTCF, EP300, ESR1, FOXA1, GATA3
colon Caco-2 CTCF
HCT-116 CTCF, TCF7L2, YY1, ZBTB33
connective tissue HVMF CTCF
embryonic stem cells H1-hESC ATF2, ATF3, BACH1, BCL11A, BRCA1, CEBPB, CHD1, CHD2, CTBP2, CTCF, EGR1, EP300, EZH2, FOSL1, GABPA, GTF2F1, HDAC2, JUN, JUND, KDM5A, MAFK, MAX, MXI1, MYC, NANOG, NRF1, POU5F1, RBBP5, REST, RFX5, RXRA, SIN3A, SIX5, SP1, SP2, SP4, SRF, SUZ12, TAF1, TAF7, TBP, TCF12, TEAD4, USF1, USF2, YY1, ZNF143
WI-38 CTCF
epithelium A549 ATF3, BCL3, BHLHE40, CEBPB, CREB1, CTCF, ELF1, EP300, ETS1, FOSL2, FOXA1, GABPA, MAX, NR3C1, REST, SIN3A, SIX5, TAF1, TCF12, USF1, YY1, ZBTB33
ECC-1 CTCF, ESR1, FOXA1, NR3C1
HCPEpiC CTCF
HEEpiC CTCF
HRE CTCF
HRPEpiC CTCF
RPTEC CTCF
SAEC CTCF
eye WERI-Rb-1 CTCF
gingival AG09319 CTCF
heart HCFaa CTCF
HCM CTCF
kidney HEK293 CTCF, ELK4, TCF7L2, TRIM28
HEK293-T-REx ZNF263
liver HepG2 ARID3A, ATF3, BHLHE40, BRCA1, CEBPB, CEBPD, CHD2, CTCF, ELF1, EP300, ESRRA, EZH2, FOSL2, FOXA1, FOXA2, GABPA, HDAC2, HNF4A, HNF4G, HSF1, IRF3, JUN, JUND, MAFF, MAFK, MAX, MAZ, MBD4, MXI1, MYBL2, MYC, NFIC, NR2C2, NR3C1, NRF1, PPARGC1A, RCOR1, REST, RFX5, RXRA, SIN3A, SP1, SP2, SREBF1, SRF, TAF1, TBP, TCF12, TCF7L2, TEAD4, USF1, USF2, YY1, ZBTB33, ZBTB7A, ZNF274
PBDEFetal GATA1
lung AG04450 CTCF
HPF CTCF
IMR90 CEBPB, CTCF, MAFK
NHLF CTCF, EZH2
muscle HSMM CTCF, EZH2
HSMMtube CTCF, EZH2
pancreas PANC-1 REST, SIN3A, TCF7L2
skin AG04449 CTCF
AG09309 CTCF
AG10803 CTCF
BJ CTCF
Fibrobl CTCF
HFF CTCF
HFF-Myc CTCF
NHDF-Ad CTCF, EZH2
NHDF-neo CTCF
NHEK CTCF, EZH2
ProgFib CTCF
testis NT2-D1 SUZ12, YY1, ZNF274
uterus HeLa-S3 BDP1, BRCA1, BRF1, BRF2, CEBPB, CHD2, CTCF, E2F1, E2F4, E2F6, ELK1, ELK4, EP300, EZH2, FOS, GABPA, GTF2F1, GTF3C2, IRF3, JUN, JUND, MAFK, MAX, MAZ, MXI1, MYC, NFYA, NFYB, NR2C2, NRF1, PRDM1, RCOR1, REST, RFX5, SMARCA4, SMARCB1, SMARCC1, SMARCC2, STAT1, STAT3, SUPT20H, TAF1, TBP, TCF7L2, TFAP2A, TFAP2C, USF2, ZKSCAN1, ZNF143, ZNF274, ZZZ3

Polymerase binding data is available for the cell types listed below.

tissue cell type polymerase binding factor
blood GM10847 POLR2A
GM12878 POLR2A, POLR3G
GM12891 POLR2A
GM12892 POLR2A
GM15510 POLR2A
GM18505 POLR2A
GM18526 POLR2A
GM18951 POLR2A
GM19099 POLR2A
GM19193 POLR2A
K562 POLR2A, POLR3A, POLR3G
NB4 POLR2A
PBDE POLR2A
Raji POLR2A
blood vessel HUVEC POLR2A
brain Gliobla POLR2A
SK-N-MC POLR2A
SK-N-SH POLR2A
U87 POLR2A
breast MCF-7 POLR2A
MCF10A-Er-Src POLR2A
colon HCT-116 POLR2A
embryonic stem cells H1-hESC POLR2A
epithelium A549 POLR2A
ECC-1 POLR2A
kidney HEK293 POLR2A
liver HepG2 POLR2A
lung IMR90 POLR2A
pancreas PANC-1 POLR2A
skin NHEK POLR2A
ProgFib POLR2A
uterus HeLa-S3 POLR2A, POLR3A

Data for other factors is available for the cell types listed below.

tissue cell type factor
blood GM12878 RAD21, SMC3, WRNIP1
K562 RAD21, SMC3
brain SK-N-SH_RA RAD21
embryonic stem cells H1-hESC RAD21
epithelium A549 RAD21
liver HepG2 RAD21, SMC3
lung IMR90 RAD21
uterus HeLa-S3 RAD21, SMC3



2. Genomatix ChIP-Seq data

The tracks in "Genomatix ChIP-Seq data" show ChIP-Seq peaks of 156 human and 31 mouse transcription factors. The references for the ChIP-Seq data are given below the transcription factor tables.

1. Human

Human transcription factor binding data is available for the cell types listed below.

tissue cell type transcription factor
blood CD133+ MEIS1, SPI1
CUTLL1 NOTCH1, RBPJ, ZNF143
GM11994 NFE2L2
GM12878 NR2C2
GM19193 RELA
Jurkat ELF1
K562 GATA1, NR2C2, STAT2
Megakaryocytes FLI1, GATA1, GATA2, RUNX1, TAL1
THP-1 VDR
bone CADO-ES1 ERG
Saos-2 TP53, TP73
brain SH-SY5Y ZNF711
SK-N-MC FLI1
breast MCF-7 AHR, ARNT, EPAS1, HIF1A, PBX1, TFAP2C
colon Caco-2 CDX2
LoVo AEBP2, ARNT, ASCL2, ATF1, ATF5, ATOH1, BARHL1, BARX2, CAMTA2, CEBPB, CEBPG, CLOCK, CREB3L4, CTCF, DBP, DLX1, E2F2, E2F3, E2F4, E2F7, E2F8, EGR1, EHF, ELF1, ESR1, ESRRA, ETS2, ETV4, ETV5, ETV7, FEV, FOXD2, FOXG1, GATA1, GATA4, GATA6, GLI2, GLI3, GLIS1, GMEB1, GMEB2, HBP1, HES2, HES4, HINFP, HNF4A, HOXA1, HOXA10, HOXA13, HOXA2, HOXA7, HOXC6, IRX3, JUN, JUND, KLF3, KLF5, LHX2, LYL1, MAZ, MECOM, MED1, MED12, MEF2C, MNT, MYB, MYBL2, MYC, MZF1, NEUROG3, NFAT5, NFE2L2, NFIL3, NFKB2, NFYA, NIPBL, NKX2-2, NPAT, NR2F1, NR2F2, NR3C1, RAD21, RARG, RBCK1, REST, RFX1, RFX2, RFX5, RXRA, SMAD2, SMAD3, SMC1A, SMC3, SOX2, SOX4, SP1, SP2, SP3, TBX3, TCF12, TCF7L2, TEAD2, TFAP2A, TFDP1, TP73, UBTF, USF2, VEZF1, YY1, ZBED4, ZBTB7B, ZFHX3, ZNF236, ZNF250, ZNF407, ZNF706
embryonic stem cells H1-hESC CTCF, NANOG, POU5F1, PRDM14
H9ES EOMES, FOXH1, SMAD3, SMAD4
gastrointestinal GIST ETV1
kidney HEK293 ETV3, HEY1, HEY2, HEYL
liver HepG2 NR2C2, USF1
lung NCI-H1819 NKX2-1
NCI-H2087 NKX2-1
NCI-H3122 FOXA1, NKX2-1
mesenchyme Rh4 PAX3
prostate C4-2B RUNX2
LNCaP NKX3-1
skin Keratinocytes TP63
uterus HeLa-S3 E2F7, MYBL2, NR2C2, TFAP2A

References:

2. Mouse

Mouse transcription factor binding data is available for the cell types listed below.

tissue cell type transcription factor
adipose 3T3-L1 Cebpb, Cebpd, Stat5a
blood B-Lymphocyte Foxo1
BMDC E2f1, E2f4, Egr1, Egr2, Ets2, Hif1a, Irf1, Irf2, Irf4, Junb, Maff, Nfkb1, Rela, Relb, Runx1, Stat1, Stat3
BMM Bcl6
G4A2 Notch1, Rbpj
HPC-7 Lyl1, Meis1
T-Lymphocyte Stat4, Stat5a, Stat5b, Stat6
T6E Notch1, Rbpj
brain P5 Atoh1
embryonic stem cells E14 E2f1, Esrrb, Klf4, Myc, Nr5a2, Pou5f1, Sox2, Stat3, Suz12, Tfcp2l1
MEF Nfic
mESC Ctcfl, Hoxb4, Jarid2
eye Retina Crx
heart HL-1 Gata4, Mef2a, Nkx2-5, Srf, Tbx5
Myocardiocytes Tbx20
kidney Nephron_progenitor Six2
liver Hepatocytes Onecut1
muscle C2C12 Myod1, Myog
Myoblast Sox6
primary_myoblasts Pax7
neuronal tissue Ainv15 Hoxc9
mNPC Sox2, Sox3
progenitor_motor_neurons Olig2
prostate prostate_cells Nkx3-1
testis embryonal_testis_cells Dmrt1
thymus Thymocyte Ikzf1, Ikzf3

References:



3. Chromatin state data

The tracks in "Chromatin states" show different chromatin states corresponding to regulatory elements such as active and inactive promoters or weakly and strongly transcribed regions.

Reference:
Jason Ernst et al. (2011).
Mapping and analysis of chromatin state dynamics in nine human cell types.
Nature 473: 43-49, [PMID: 21441907].

Chromatin state data is available for the cell types listed below.

tissue cell type
blood Gm12878, K562
blood vessel Huvec
breast Hmec
embryonic stem cells H1hesc
liver Hepg2
lung Nhlf
muscle Hsmm
skin Nhek



4. Evolutionary constrained elements

The tracks in "Evolutionary constrained elements" show evolutionary constrained elements according to Kerstin Lindblad-Toh et al. (2011). Kerstin Lindblad-Toh et al. compared the human genome sequence with 29 mammalian genome sequences and identified 4.2% of the human genome as evolutionary constrained.

Reference:
Kerstin Lindblad-Toh et al. (2011).
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature 478: 476-482, [PMID: 21993624].