General Details

Super-enhancer:SE_00_02600833
Genomic Locus: chr12: 52418989-52438968
Size/Length:19979bp
Conservation:0.0876592
BioSample Type:Tissue
Tissue Type:Muscle of trunk
Sample Name:muscle-of-trunk
Source:Roadmap
Element:4
Rank:833
ChIP Density(Case):12502.8582
ChIP Density(Input):1832.0743

Super-enhancer Associated Network


* The complex regulatory networks formed by this SE , SE associated genes , TFs binding to the SE and their upstream pathways can be interactively visualized.


Fimo:
SE-Gene Linking Strategies:
Pathway Enriciment Threshold:
Top Pathway:
 



Super-enhancer Associated Statistics

Associated Gene Details

ROSE Overlap:.
ROSE Proximal:C12orf44,NR4A1,GRASP
ROSE Closest:NR4A1
The Closest Active:NR4A1

Factors Binding to Super-enhancer




Using these SE element regions to analyze by online tools GREAT *The TFs binding to this SE identified by ChIP-seq.

Chrome Element_Start Element_End TF TF Source TF_Start TF_End TF Class Master TF

Using these SE element regions to analyze by online tools GREAT * The TFs binding to this SE predicted by Motif.

Chrome Element_Start Element_End TF Database TF_Start TF_End Score P_Value TF Class Master TF
chr12 52428472 52430911 CDX2 Transfac.V$CDX2_Q5_01 52429109 52429119 13.32320 6.3e-07 Helix-turn-helix domains N
chr12 52418989 52421174 CTCF Transfac.V$CTCF_01 52419606 52419625 21.22920 1.53e-08 Zinc-coordinating DNA-binding domains N
chr12 52418989 52421174 CTCF Transfac.V$CTCF_02 52419604 52419623 20.38810 2.03e-08 Zinc-coordinating DNA-binding domains N
chr12 52418989 52421174 CTCF JASPAR2014.MA0139.1 52419607 52419625 22.01610 1.41e-08 Zinc-coordinating DNA-binding domains N
chr12 52436723 52438968 ELF3 Transfac.V$ELF4_04 52438329 52438345 14.81010 2.51e-07 Helix-turn-helix domains N
chr12 52436723 52438968 ELF3 Uniprobe.UP00407_2 52438329 52438345 14.69270 2.8e-07 Helix-turn-helix domains N
chr12 52418989 52421174 GATA1 Transfac.V$GATA1_03 52419750 52419763 14.78180 8.85e-07 Zinc-coordinating DNA-binding domains N
chr12 52425852 52428176 HENMT1 Transfac.V$HEN1_01 52426980 52427001 17.57830 7.29e-07 UNKNOW N
chr12 52436723 52438968 IRF7 Transfac.V$IRF7_01 52438462 52438479 18.00000 1.98e-07 Helix-turn-helix domains N
chr12 52436723 52438968 MAZ Transfac.V$MAZ_Q6_01 52436811 52436824 16.62640 7.02e-07 Zinc-coordinating DNA-binding domains N
chr12 52436723 52438968 MAZ Transfac.V$MAZ_Q6_01 52438761 52438774 16.53850 8e-07 Zinc-coordinating DNA-binding domains N
chr12 52428472 52430911 MEF2A Transfac.V$MEF2A_03 52430822 52430833 19.48390 3.1e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2A Transfac.V$MEF2A_Q6 52430824 52430833 15.06060 8.34e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2A Jolma2013.MEF2A_DBD 52430822 52430833 19.41410 3.1e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2B Transfac.V$MEF2B_01 52430822 52430833 20.70910 1.09e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2B Jolma2013.MEF2B_full 52430822 52430833 20.63640 1.09e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2D Transfac.V$MEF2D_01 52430822 52430833 19.80000 5.17e-07 alpha-Helices exposed by beta-structures N
chr12 52428472 52430911 MEF2D Jolma2013.MEF2D_DBD 52430822 52430833 19.75760 5.17e-07 alpha-Helices exposed by beta-structures N
chr12 52425852 52428176 MTF1 Transfac.V$MTF1_06 52426483 52426496 13.43840 4.42e-08 Zinc-coordinating DNA-binding domains N
chr12 52425852 52428176 MTF1 Uniprobe.UP00097_2 52426483 52426496 13.39730 4.42e-08 Zinc-coordinating DNA-binding domains N
chr12 52428472 52430911 NFE2L1 Transfac.V$TCF11_01 52429394 52429406 12.40000 8.29e-08 Basic domains N
chr12 52418989 52421174 NKX2-3 Transfac.V$NKX23_01 52420262 52420277 17.82000 2.47e-07 Helix-turn-helix domains N
chr12 52418989 52421174 NKX2-3 Homeodomain.UP00190_1 52420262 52420277 17.88390 2.3e-07 Helix-turn-helix domains N
chr12 52418989 52421174 NKX2-3 Uniprobe.UP00190_1 52420262 52420277 17.88390 2.3e-07 Helix-turn-helix domains N
chr12 52418989 52421174 NKX3-2 Transfac.V$NKX32_02 52420260 52420276 16.49490 9.05e-07 Helix-turn-helix domains N
chr12 52418989 52421174 NKX3-2 Homeodomain.UP00228_1 52420260 52420276 16.45450 9.51e-07 Helix-turn-helix domains N
chr12 52418989 52421174 NKX3-2 Uniprobe.UP00228_1 52420260 52420276 16.45450 9.51e-07 Helix-turn-helix domains N
chr12 52428472 52430911 NR3C1 Transfac.V$NR3C1_01 52429975 52429992 16.89290 9.04e-07 Zinc-coordinating DNA-binding domains N
chr12 52436723 52438968 PHOX2B Transfac.V$PMX2B_01 52438822 52438838 17.01000 9.21e-07 Helix-turn-helix domains N
chr12 52436723 52438968 PHOX2B Homeodomain.UP00149_1 52438822 52438838 16.95500 9.56e-07 Helix-turn-helix domains N
chr12 52436723 52438968 PHOX2B Uniprobe.UP00149_1 52438822 52438838 16.95500 9.56e-07 Helix-turn-helix domains N
chr12 52418989 52421174 PITX2 Transfac.V$PITX2_Q2 52419110 52419120 16.09090 8.91e-07 Helix-turn-helix domains N
chr12 52418989 52421174 PITX2 Transfac.V$PITX2_Q6 52419111 52419120 15.07070 9.1e-07 Helix-turn-helix domains N
chr12 52418989 52421174 POLR3A Transfac.V$RPC155_01 52419058 52419073 23.71200 2.42e-10 ENCODE_TF N
chr12 52418989 52421174 POU3F4 Transfac.V$POU3F4_03 52420012 52420022 17.22400 2.04e-07 Helix-turn-helix domains N
chr12 52418989 52421174 POU3F4 Jolma2013.POU3F4_DBD_2 52420012 52420022 17.18400 2.04e-07 Helix-turn-helix domains N
chr12 52418989 52421174 POU4F1 Transfac.V$POU4F1_Q6 52420012 52420022 15.52730 2.04e-07 Helix-turn-helix domains N
chr12 52418989 52421174 POU6F1 Transfac.V$POU6F1_01 52420011 52420021 18.87880 4.08e-07 Helix-turn-helix domains N
chr12 52428472 52430911 RREB1 Transfac.V$RREB1_01 52429871 52429884 19.02730 3.15e-07 Zinc-coordinating DNA-binding domains Y
chr12 52436723 52438968 SHOX2 Transfac.V$SHOX2_01 52438821 52438837 16.14000 7.83e-07 Helix-turn-helix domains N
chr12 52436723 52438968 SHOX2 Transfac.V$SHOX2_01 52438822 52438838 16.40000 4.81e-07 Helix-turn-helix domains N
chr12 52436723 52438968 SHOX2 Homeodomain.UP00257_1 52438821 52438837 16.09910 8.16e-07 Helix-turn-helix domains N
chr12 52436723 52438968 SHOX2 Homeodomain.UP00257_1 52438822 52438838 16.37840 4.82e-07 Helix-turn-helix domains N
chr12 52436723 52438968 SHOX2 Uniprobe.UP00257_1 52438821 52438837 16.09910 8.16e-07 Helix-turn-helix domains N
chr12 52436723 52438968 SHOX2 Uniprobe.UP00257_1 52438822 52438838 16.37840 4.82e-07 Helix-turn-helix domains N
chr12 52428472 52430911 SLC20A1 Transfac.V$PIT1_Q6 52429509 52429526 17.68000 2.37e-07 UNKNOW N
chr12 52418989 52421174 SOX17 Transfac.V$SOX17_04 52419983 52419999 13.90230 6.34e-07 Other all-alpha-helical DNA-binding domains N
chr12 52418989 52421174 SOX17 Uniprobe.UP00014_2 52419983 52419999 13.89100 6.49e-07 Other all-alpha-helical DNA-binding domains N
chr12 52418989 52421174 SOX8 Uniprobe.UP00051_2 52419982 52419995 14.28470 9.93e-07 Other all-alpha-helical DNA-binding domains N
chr12 52428472 52430911 SP1 Transfac.V$SP1_Q6 52430788 52430800 15.96100 6.77e-07 Zinc-coordinating DNA-binding domains N
chr12 52425852 52428176 SP4 Transfac.V$SP4_Q5 52427718 52427728 16.85000 9.09e-07 Zinc-coordinating DNA-binding domains N
chr12 52428472 52430911 SP4 Transfac.V$SP4_Q5 52430789 52430799 17.39000 6.06e-07 Zinc-coordinating DNA-binding domains N
chr12 52428472 52430911 TBX5 Transfac.V$TBX5_Q5 52430693 52430702 18.51820 9.51e-07 Immunoglobulin fold N
chr12 52418989 52421174 TCF3 Transfac.V$E2A_Q2 52419085 52419098 15.94950 3.57e-07 Basic domains N
chr12 52436723 52438968 TFAP4 Transfac.V$AP4_Q6_02 52437840 52437852 14.95000 3.92e-07 Basic domains Y
chr12 52436723 52438968 UNCX Homeodomain.UP00142_1 52438822 52438838 17.13510 8.42e-07 Helix-turn-helix domains N
chr12 52436723 52438968 UNCX Uniprobe.UP00142_1 52438822 52438838 17.13510 8.42e-07 Helix-turn-helix domains N
chr12 52418989 52421174 ZBTB7B Transfac.V$ZBTB7B_03 52420851 52420865 15.89160 7.26e-07 Zinc-coordinating DNA-binding domains N
chr12 52418989 52421174 ZBTB7B Uniprobe.UP00047_1 52420851 52420865 15.82880 6.88e-07 Zinc-coordinating DNA-binding domains N
chr12 52436723 52438968 ZNF263 JASPAR2014.MA0528.1 52438761 52438781 19.04000 1.68e-07 Zinc-coordinating DNA-binding domains N

The Upstream Pathways of TFs Binding to SE



TF Pathway ID Pathway Name Source
CDX2 pathway0001702 POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation Reactome
CDX2 pathway0002181 Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) Reactome
CTCF pathway0000061 Activation of anterior HOX genes in hindbrain development during early embryogenesis Reactome
CTCF pathway0002222 TGF_beta_Receptor NetPath
ELF3 pathway0000658 EGFR1 NetPath
ELF3 pathway0001604 PDGF signaling pathway PANTHER
GATA1 pathway0000335 C-MYB transcription factor network PID
GATA1 pathway0000747 Factors involved in megakaryocyte development and platelet production Reactome
GATA1 pathway0001126 IL3 NetPath
GATA1 pathway0001516 Notch-mediated HES/HEY network PID
GATA1 pathway0001582 p73 transcription factor network PID
GATA1 pathway0002033 Signaling events mediated by HDAC Class I PID
GATA1 pathway0002034 Signaling events mediated by HDAC Class II PID
HENMT1 pathway0001666 PIWI-interacting RNA (piRNA) biogenesis Reactome
IRF7 pathway0000070 Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon Reactome
IRF7 pathway0000590 DEx/H-box helicases activate type I IFN and inflammatory cytokines production Reactome
IRF7 pathway0000747 Factors involved in megakaryocyte development and platelet production Reactome
IRF7 pathway0001180 Interferon alpha/beta signaling Reactome
IRF7 pathway0001181 Interferon gamma signaling Reactome
IRF7 pathway0001849 Regulation of nuclear SMAD2/3 signaling PID
IRF7 pathway0002278 TRAF3-dependent IRF activation pathway Reactome
IRF7 pathway0002282 TRAF6 mediated IRF7 activation Reactome
IRF7 pathway0002283 TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling Reactome
IRF7 pathway0002602 Toll-like receptor signaling pathway KEGG
IRF7 pathway0002604 RIG-I-like receptor signaling pathway KEGG
IRF7 pathway0002605 Cytosolic DNA-sensing pathway KEGG
IRF7 pathway0002655 Hepatitis C KEGG
IRF7 pathway0002754 Hs_Structural_Pathway_of_Interleukin_1_(IL-1)_WP2637_87707 WikiPathways
IRF7 pathway0002795 Hs_Regulation_of_toll-like_receptor_signaling_pathway_WP1449_81172 WikiPathways
IRF7 pathway0002796 Hs_Toll-like_Receptor_Signaling_Pathway_WP75_83867 WikiPathways
IRF7 pathway0002845 Hs_TLR4_Signaling_and_Tolerance_WP3851_90114 WikiPathways
MEF2A pathway0000393 CDO in myogenesis Reactome
MEF2A pathway0000715 ERK/MAPK targets Reactome
MEF2A pathway0002044 Signaling mediated by p38-alpha and p38-beta PID
MEF2A pathway0002222 TGF_beta_Receptor NetPath
MEF2A pathway0002782 Hs_p38_MAPK_Signaling_Pathway_WP400_72084 WikiPathways
MEF2B pathway0000393 CDO in myogenesis Reactome
MEF2B pathway0001572 p38 MAPK pathway PANTHER
MEF2D pathway0000393 CDO in myogenesis Reactome
MEF2D pathway0000430 Circadian Clock Reactome
MEF2D pathway0001572 p38 MAPK pathway PANTHER
MEF2D pathway0001935 Role of Calcineurin-dependent NFAT signaling in lymphocytes PID
MEF2D pathway0002035 Signaling events mediated by HDAC Class III PID
MEF2D pathway0002299 Transcriptional activation of mitochondrial biogenesis Reactome
MTF1 pathway0000069 Activation of gene expression by SREBF (SREBP) Reactome
MTF1 pathway0001704 PPARA activates gene expression Reactome
NKX3-2 pathway0002725 Hs_Endochondral_Ossification_WP474_87977 WikiPathways
NR3C1 pathway0000176 AndrogenReceptor NetPath
NR3C1 pathway0000187 AP-1 transcription factor network PID
NR3C1 pathway0000316 BMAL1:CLOCK,NPAS2 activates circadian gene expression Reactome
NR3C1 pathway0000401 Cellular roles of Anthrax toxin PID
NR3C1 pathway0000825 FOXA2 and FOXA3 transcription factor networks PID
NR3C1 pathway0000916 Glucocorticoid receptor regulatory network PID
NR3C1 pathway0001120 IL2 NetPath
NR3C1 pathway0001534 Nuclear Receptor transcription pathway Reactome
NR3C1 pathway0001744 PTK6 Expression Reactome
NR3C1 pathway0001825 Regulation of Androgen receptor activity PID
NR3C1 pathway0001849 Regulation of nuclear SMAD2/3 signaling PID
NR3C1 pathway0002034 Signaling events mediated by HDAC Class II PID
NR3C1 pathway0002570 Neuroactive ligand-receptor interaction KEGG
NR3C1 pathway0002740 Hs_Endoderm_Differentiation_WP2853_88152 WikiPathways
NR3C1 pathway0002750 Hs_Serotonin_Receptor_4-6-7_and_NR3C_Signaling_WP734_74438 WikiPathways
NR3C1 pathway0002755 Hs_White_fat_cell_differentiation_WP3946_90940 WikiPathways
NR3C1 pathway0002808 Hs_Transcription_factor_regulation_in_adipogenesis_WP3599_88581 WikiPathways
NR3C1 pathway0002812 Hs_Sudden_Infant_Death_Syndrome_(SIDS)_Susceptibility_Pathways_WP706_86078 WikiPathways
PHOX2B pathway0002747 Hs_Neural_Crest_Differentiation_WP2064_79263 WikiPathways
PITX2 pathway0001848 Regulation of nuclear beta catenin signaling and target gene transcription PID
PITX2 pathway0002591 TGF-beta signaling pathway KEGG
PITX2 pathway0002768 Hs_Heart_Development_WP1591_90186 WikiPathways
PITX2 pathway0002771 Hs_BMP_Signaling_Pathway_in_Eyelid_Development_WP3927_90735 WikiPathways
POLR3A pathway0000532 Cytosolic sensors of pathogen-associated DNA Reactome
POLR3A pathway0001926 RNA Polymerase III Abortive And Retractive Initiation Reactome
POLR3A pathway0001927 RNA Polymerase III Chain Elongation Reactome
POLR3A pathway0001928 RNA Polymerase III Transcription Initiation From Type 1 Promoter Reactome
POLR3A pathway0001929 RNA Polymerase III Transcription Initiation From Type 2 Promoter Reactome
POLR3A pathway0001930 RNA Polymerase III Transcription Initiation From Type 3 Promoter Reactome
POLR3A pathway0001931 RNA Polymerase III Transcription Termination Reactome
POLR3A pathway0002492 Purine metabolism KEGG
POLR3A pathway0002494 Pyrimidine metabolism KEGG
POLR3A pathway0002605 Cytosolic DNA-sensing pathway KEGG
POU4F1 pathway0000608 Direct p53 effectors PID
POU4F1 pathway0001864 Regulation of TP53 Activity through Association with Co-factors Reactome
POU4F1 pathway0002388 Validated nuclear estrogen receptor alpha network PID
SOX17 pathway0000549 Deactivation of the beta-catenin transactivating complex Reactome
SOX17 pathway0002587 Wnt signaling pathway KEGG
SOX17 pathway0002740 Hs_Endoderm_Differentiation_WP2853_88152 WikiPathways
SP1 pathway0000069 Activation of gene expression by SREBF (SREBP) Reactome
SP1 pathway0000176 AndrogenReceptor NetPath
SP1 pathway0000187 AP-1 transcription factor network PID
SP1 pathway0000335 C-MYB transcription factor network PID
SP1 pathway0000608 Direct p53 effectors PID
SP1 pathway0000648 E2F transcription factor network PID
SP1 pathway0000658 EGFR1 NetPath
SP1 pathway0000824 FOXA1 transcription factor network PID
SP1 pathway0000825 FOXA2 and FOXA3 transcription factor networks PID
SP1 pathway0000826 FOXM1 transcription factor network PID
SP1 pathway0001021 HIF-1-alpha transcription factor network PID
SP1 pathway0001022 HIF-2-alpha transcription factor network PID
SP1 pathway0001046 Huntington disease PANTHER
SP1 pathway0001122 IL2 signaling events mediated by STAT5 PID
SP1 pathway0001127 IL4-mediated signaling events PID
SP1 pathway0001264 Leptin NetPath
SP1 pathway0001543 Oncogene Induced Senescence Reactome
SP1 pathway0001582 p73 transcription factor network PID
SP1 pathway0001704 PPARA activates gene expression Reactome
SP1 pathway0001849 Regulation of nuclear SMAD2/3 signaling PID
SP1 pathway0001861 Regulation of Telomerase PID
SP1 pathway0001921 RNA polymerase II transcribes snRNA genes Reactome
SP1 pathway0002069 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription Reactome
SP1 pathway0002222 TGF_beta_Receptor NetPath
SP1 pathway0002391 Validated targets of C-MYC transcriptional repression PID
SP1 pathway0002392 Validated transcriptional targets of AP1 family members Fra1 and Fra2 PID
SP1 pathway0002394 Validated transcriptional targets of TAp63 isoforms PID
SP1 pathway0002591 TGF-beta signaling pathway KEGG
SP1 pathway0002642 Huntington's disease KEGG
SP1 pathway0002699 Hs_Corticotropin-releasing_hormone_signaling_pathway_WP2355_90017 WikiPathways
SP1 pathway0002712 Hs_Leptin_signaling_pathway_WP2034_89856 WikiPathways
SP1 pathway0002718 Hs_Interleukin-11_Signaling_Pathway_WP2332_79525 WikiPathways
SP1 pathway0002731 Hs_Integrated_Breast_Cancer_Pathway_WP1984_82941 WikiPathways
SP1 pathway0002811 Hs_Estrogen_signaling_pathway_WP712_78491 WikiPathways
SP1 pathway0002812 Hs_Sudden_Infant_Death_Syndrome_(SIDS)_Susceptibility_Pathways_WP706_86078 WikiPathways
SP1 pathway0002853 Hs_TGF-beta_Signaling_Pathway_WP366_90028 WikiPathways
SP1 pathway0002862 Hs_AGE-RAGE_pathway_WP2324_89798 WikiPathways
SP1 pathway0002863 Hs_Androgen_receptor_signaling_pathway_WP138_79958 WikiPathways
SP1 pathway0002866 Hs_EGF-EGFR_Signaling_Pathway_WP437_79266 WikiPathways
TBX5 pathway0001649 Physiological factors Reactome
TBX5 pathway0002460 YAP1- and WWTR1 (TAZ)-stimulated gene expression Reactome
TBX5 pathway0002768 Hs_Heart_Development_WP1591_90186 WikiPathways
TCF3 pathway0000393 CDO in myogenesis Reactome
TCF3 pathway0001078 ID NetPath
TCF3 pathway0001516 Notch-mediated HES/HEY network PID
TCF3 pathway0001517 Notch NetPath
TCF3 pathway0001574 p38 signaling mediated by MAPKAP kinases PID
TCF3 pathway0001849 Regulation of nuclear SMAD2/3 signaling PID
TCF3 pathway0002439 Wnt NetPath
TCF3 pathway0002841 Hs_Ectoderm_Differentiation_WP2858_89329 WikiPathways
ZBTB7B pathway0002841 Hs_Ectoderm_Differentiation_WP2858_89329 WikiPathways
ZNF263 pathway0000905 Generic Transcription Pathway Reactome