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ENCODE: H3K4me1 ChIP-Seq of primary human cells
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Results for SMAD2
Z-value: 1.83
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Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:
This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.
For each TF, only the top 5 correlated CREs are shown.
| CRE | Gene | Distance | Association probability | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|---|---|
| chr18_45440567_45440723 | SMAD2 | 9368 | 0.253140 | 0.88 | 1.6e-03 | Click! |
| chr18_45448479_45448730 | SMAD2 | 1409 | 0.525243 | 0.83 | 5.9e-03 | Click! |
| chr18_45450122_45450273 | SMAD2 | 184 | 0.965160 | 0.94 | 2.0e-04 | Click! |
| chr18_45453074_45453280 | SMAD2 | 3164 | 0.333846 | 0.92 | 4.8e-04 | Click! |
| chr18_45453396_45453906 | SMAD2 | 3082 | 0.337865 | 0.82 | 6.4e-03 | Click! |
Showing 1 to 5 of 5 entries
Top target CREs of the motif:
| Cis Regulatory Element (CRE) | Target Score | Top associated gene | Gene Info | Distance of CRE to TSS | CRE/Gene association probability |
|---|---|---|---|---|---|
| chr20_44688889_44689146 | 0.60 |
NCOA5 |
nuclear receptor coactivator 5 |
29574 |
0.11 |
| chrX_14515561_14515762 | 0.58 |
GLRA2 |
glycine receptor, alpha 2 |
31759 |
0.25 |
| chr22_30699298_30699467 | 0.52 |
TBC1D10A |
TBC1 domain family, member 10A |
2238 |
0.16 |
| chr15_70383895_70384046 | 0.47 |
TLE3 |
transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila) |
3154 |
0.3 |
| chr14_21492164_21492434 | 0.47 |
NDRG2 |
NDRG family member 2 |
44 |
0.94 |
| chr18_21293009_21293241 | 0.46 |
LAMA3 |
laminin, alpha 3 |
23477 |
0.2 |
| chr21_45566060_45566211 | 0.45 |
C21orf33 |
chromosome 21 open reading frame 33 |
10134 |
0.15 |
| chr22_36055457_36055755 | 0.43 |
APOL6 |
apolipoprotein L, 6 |
11164 |
0.18 |
| chr3_50611942_50612149 | 0.43 |
HEMK1 |
HemK methyltransferase family member 1 |
2510 |
0.21 |
| chr2_68995898_68996135 | 0.43 |
ARHGAP25 |
Rho GTPase activating protein 25 |
5917 |
0.26 |
Histogram of CRE-TSS distances for CREs targeted by :
Rank distribution of CRE target scores:
Distribution of target CREs across different genomic regions:
Network of associatons between targets according to the STRING database.
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.5 | GO:0031295 | lymphocyte costimulation(GO:0031294) T cell costimulation(GO:0031295) |
| 0.0 | 2.1 | GO:0050852 | T cell receptor signaling pathway(GO:0050852) |
| 0.0 | 2.1 | GO:0051056 | regulation of small GTPase mediated signal transduction(GO:0051056) |
| 0.0 | 1.4 | GO:0018279 | peptidyl-asparagine modification(GO:0018196) protein N-linked glycosylation via asparagine(GO:0018279) |
| 0.1 | 0.7 | GO:0002710 | negative regulation of T cell mediated immunity(GO:0002710) |
| 0.1 | 0.7 | GO:0031648 | protein destabilization(GO:0031648) |
| 0.0 | 0.7 | GO:0043966 | histone H3 acetylation(GO:0043966) |
| 0.0 | 0.7 | GO:1904667 | negative regulation of ubiquitin protein ligase activity(GO:1904667) |
| 0.1 | 0.6 | GO:0033152 | immunoglobulin V(D)J recombination(GO:0033152) |
| 0.1 | 0.6 | GO:0030206 | chondroitin sulfate biosynthetic process(GO:0030206) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 2.3 | GO:0009897 | external side of plasma membrane(GO:0009897) |
| 0.0 | 2.1 | GO:0030173 | integral component of Golgi membrane(GO:0030173) |
| 0.0 | 1.2 | GO:0005681 | spliceosomal complex(GO:0005681) |
| 0.0 | 1.0 | GO:0042470 | melanosome(GO:0042470) pigment granule(GO:0048770) |
| 0.0 | 0.8 | GO:0031461 | cullin-RING ubiquitin ligase complex(GO:0031461) |
| 0.0 | 0.8 | GO:0044815 | nucleosome(GO:0000786) DNA packaging complex(GO:0044815) |
| 0.1 | 0.7 | GO:0001891 | phagocytic cup(GO:0001891) |
| 0.0 | 0.7 | GO:0016514 | SWI/SNF complex(GO:0016514) |
| 0.0 | 0.7 | GO:0019005 | SCF ubiquitin ligase complex(GO:0019005) |
| 0.0 | 0.7 | GO:0030175 | filopodium(GO:0030175) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 3.3 | GO:0016563 | obsolete transcription activator activity(GO:0016563) |
| 0.0 | 2.0 | GO:0003702 | obsolete RNA polymerase II transcription factor activity(GO:0003702) |
| 0.0 | 1.6 | GO:0005070 | SH3/SH2 adaptor activity(GO:0005070) |
| 0.1 | 1.3 | GO:0008373 | sialyltransferase activity(GO:0008373) |
| 0.0 | 1.2 | GO:0008301 | DNA binding, bending(GO:0008301) |
| 0.1 | 1.1 | GO:0043027 | cysteine-type endopeptidase inhibitor activity involved in apoptotic process(GO:0043027) |
| 0.0 | 1.0 | GO:0004715 | non-membrane spanning protein tyrosine kinase activity(GO:0004715) |
| 0.1 | 0.9 | GO:0004697 | protein kinase C activity(GO:0004697) |
| 0.0 | 0.8 | GO:0043621 | protein self-association(GO:0043621) |
| 0.0 | 0.7 | GO:0001540 | beta-amyloid binding(GO:0001540) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 3.9 | PID TCR PATHWAY | TCR signaling in naïve CD4+ T cells |
| 0.0 | 1.8 | PID NFAT TFPATHWAY | Calcineurin-regulated NFAT-dependent transcription in lymphocytes |
| 0.1 | 1.6 | PID IL2 PI3K PATHWAY | IL2 signaling events mediated by PI3K |
| 0.0 | 1.4 | PID NFAT 3PATHWAY | Role of Calcineurin-dependent NFAT signaling in lymphocytes |
| 0.1 | 1.2 | PID TCR JNK PATHWAY | JNK signaling in the CD4+ TCR pathway |
| 0.0 | 1.1 | SIG PIP3 SIGNALING IN B LYMPHOCYTES | Genes related to PIP3 signaling in B lymphocytes |
| 0.0 | 0.8 | PID HIF2PATHWAY | HIF-2-alpha transcription factor network |
| 0.0 | 0.7 | PID INSULIN PATHWAY | Insulin Pathway |
| 0.0 | 0.6 | PID PI3KCI PATHWAY | Class I PI3K signaling events |
| 0.0 | 0.6 | PID LKB1 PATHWAY | LKB1 signaling events |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 2.5 | REACTOME GENERATION OF SECOND MESSENGER MOLECULES | Genes involved in Generation of second messenger molecules |
| 0.0 | 1.3 | REACTOME IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL | Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |
| 0.0 | 1.1 | REACTOME G1 PHASE | Genes involved in G1 Phase |
| 0.0 | 1.1 | REACTOME GLYCOSPHINGOLIPID METABOLISM | Genes involved in Glycosphingolipid metabolism |
| 0.0 | 1.1 | REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA | Genes involved in Processing of Capped Intron-Containing Pre-mRNA |
| 0.1 | 0.9 | REACTOME N GLYCAN ANTENNAE ELONGATION | Genes involved in N-Glycan antennae elongation |
| 0.0 | 0.9 | REACTOME ACTIVATION OF NF KAPPAB IN B CELLS | Genes involved in Activation of NF-kappaB in B Cells |
| 0.0 | 0.9 | REACTOME RESPIRATORY ELECTRON TRANSPORT ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING AND HEAT PRODUCTION BY UNCOUPLING PROTEINS | Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. |
| 0.0 | 0.8 | REACTOME PLATELET CALCIUM HOMEOSTASIS | Genes involved in Platelet calcium homeostasis |
| 0.0 | 0.8 | REACTOME MEIOTIC SYNAPSIS | Genes involved in Meiotic Synapsis |