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ENCODE: H3K4me1 ChIP-Seq of primary human cells
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Results for TBX3
Z-value: 3.68
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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 |
|---|---|---|---|---|---|---|
| chr12_115110030_115110181 | TBX3 | 11290 | 0.213731 | -0.56 | 1.2e-01 | Click! |
| chr12_115121939_115122144 | TBX3 | 72 | 0.978742 | 0.55 | 1.3e-01 | Click! |
| chr12_115123012_115123311 | TBX3 | 1192 | 0.537659 | -0.48 | 1.9e-01 | Click! |
| chr12_115123320_115123471 | TBX3 | 1426 | 0.474004 | -0.60 | 8.7e-02 | Click! |
| chr12_115130647_115130798 | TBX3 | 8753 | 0.227867 | -0.46 | 2.1e-01 | 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 |
|---|---|---|---|---|---|
| chr10_14610353_14610666 | 1.24 |
FAM107B |
family with sequence similarity 107, member B |
3520 |
0.31 |
| chr7_150364153_150364486 | 1.18 |
GIMAP2 |
GTPase, IMAP family member 2 |
18469 |
0.16 |
| chr5_90730851_90731207 | 1.10 |
ARRDC3 |
arrestin domain containing 3 |
51853 |
0.17 |
| chr11_122943932_122944158 | 1.09 |
HSPA8 |
heat shock 70kDa protein 8 |
10107 |
0.15 |
| chr17_81005533_81005684 | 1.07 |
B3GNTL1 |
UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 |
1434 |
0.46 |
| chr11_35147334_35147528 | 1.03 |
AL356215.1 |
|
2784 |
0.24 |
| chr1_154438581_154439022 | 0.97 |
RP11-350G8.9 |
|
13687 |
0.12 |
| chr6_152507132_152507415 | 0.97 |
SYNE1 |
spectrin repeat containing, nuclear envelope 1 |
17774 |
0.28 |
| chr16_68115229_68115482 | 0.94 |
NFATC3 |
nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3 |
3892 |
0.13 |
| chr12_50064173_50064541 | 0.92 |
FMNL3 |
formin-like 3 |
36646 |
0.11 |
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 | 5.3 | GO:0006397 | mRNA processing(GO:0006397) |
| 0.1 | 5.0 | GO:0050851 | antigen receptor-mediated signaling pathway(GO:0050851) |
| 0.0 | 4.6 | GO:0006412 | translation(GO:0006412) |
| 0.2 | 4.4 | GO:0050690 | regulation of defense response to virus by virus(GO:0050690) |
| 0.4 | 3.2 | GO:0007172 | signal complex assembly(GO:0007172) |
| 0.1 | 2.4 | GO:0045576 | mast cell activation(GO:0045576) |
| 0.0 | 2.4 | GO:0018196 | peptidyl-asparagine modification(GO:0018196) protein N-linked glycosylation via asparagine(GO:0018279) |
| 0.4 | 2.1 | GO:0002710 | negative regulation of T cell mediated immunity(GO:0002710) |
| 0.1 | 2.1 | GO:0050772 | positive regulation of axonogenesis(GO:0050772) |
| 0.5 | 2.0 | GO:0030854 | positive regulation of granulocyte differentiation(GO:0030854) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.7 | GO:0005730 | nucleolus(GO:0005730) |
| 0.0 | 5.5 | GO:0009897 | external side of plasma membrane(GO:0009897) |
| 0.0 | 3.0 | GO:0005938 | cell cortex(GO:0005938) cytoplasmic region(GO:0099568) |
| 0.1 | 2.4 | GO:0030173 | integral component of Golgi membrane(GO:0030173) |
| 0.1 | 2.0 | GO:0005942 | phosphatidylinositol 3-kinase complex(GO:0005942) |
| 0.1 | 2.0 | GO:0030175 | filopodium(GO:0030175) |
| 0.2 | 1.9 | GO:0001772 | immunological synapse(GO:0001772) |
| 0.2 | 1.9 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
| 0.0 | 1.9 | GO:0055037 | recycling endosome(GO:0055037) |
| 0.1 | 1.7 | GO:0005876 | spindle microtubule(GO:0005876) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 9.3 | GO:0003723 | RNA binding(GO:0003723) |
| 0.0 | 5.4 | GO:0005525 | GTP binding(GO:0005525) |
| 0.0 | 3.6 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.1 | 3.5 | GO:0004715 | non-membrane spanning protein tyrosine kinase activity(GO:0004715) |
| 0.2 | 3.4 | GO:0043027 | cysteine-type endopeptidase inhibitor activity involved in apoptotic process(GO:0043027) |
| 0.3 | 3.2 | GO:0004697 | protein kinase C activity(GO:0004697) |
| 0.1 | 3.1 | GO:0101005 | thiol-dependent ubiquitin-specific protease activity(GO:0004843) thiol-dependent ubiquitinyl hydrolase activity(GO:0036459) ubiquitinyl hydrolase activity(GO:0101005) |
| 0.1 | 3.0 | GO:0005070 | SH3/SH2 adaptor activity(GO:0005070) |
| 0.2 | 2.9 | GO:0030159 | receptor signaling complex scaffold activity(GO:0030159) |
| 0.3 | 2.7 | GO:0016493 | C-C chemokine receptor activity(GO:0016493) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 14.9 | PID CD8 TCR PATHWAY | TCR signaling in naïve CD8+ T cells |
| 0.1 | 6.3 | PID NFAT TFPATHWAY | Calcineurin-regulated NFAT-dependent transcription in lymphocytes |
| 0.2 | 4.4 | PID EPHRINB REV PATHWAY | Ephrin B reverse signaling |
| 0.1 | 3.6 | PID NFAT 3PATHWAY | Role of Calcineurin-dependent NFAT signaling in lymphocytes |
| 0.1 | 3.4 | PID IL8 CXCR2 PATHWAY | IL8- and CXCR2-mediated signaling events |
| 0.2 | 3.3 | PID TCR PATHWAY | TCR signaling in naïve CD4+ T cells |
| 0.1 | 2.4 | PID AR TF PATHWAY | Regulation of Androgen receptor activity |
| 0.2 | 2.3 | SA PTEN PATHWAY | PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. |
| 0.2 | 2.3 | SA MMP CYTOKINE CONNECTION | Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. |
| 0.2 | 2.1 | SA FAS SIGNALING | The TNF-type receptor Fas induces apoptosis on ligand binding. |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 6.9 | REACTOME GENERATION OF SECOND MESSENGER MOLECULES | Genes involved in Generation of second messenger molecules |
| 0.1 | 3.9 | REACTOME SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE | Genes involved in Synthesis of PIPs at the plasma membrane |
| 0.1 | 3.7 | REACTOME INTERFERON GAMMA SIGNALING | Genes involved in Interferon gamma signaling |
| 0.3 | 3.6 | REACTOME CD28 DEPENDENT VAV1 PATHWAY | Genes involved in CD28 dependent Vav1 pathway |
| 0.1 | 3.6 | REACTOME IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL | Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |
| 0.1 | 3.2 | REACTOME EFFECTS OF PIP2 HYDROLYSIS | Genes involved in Effects of PIP2 hydrolysis |
| 0.1 | 2.7 | REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE | Genes involved in Sema4D induced cell migration and growth-cone collapse |
| 0.2 | 2.6 | REACTOME N GLYCAN ANTENNAE ELONGATION | Genes involved in N-Glycan antennae elongation |
| 0.0 | 2.5 | 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. |
| 0.2 | 2.3 | REACTOME IL 7 SIGNALING | Genes involved in Interleukin-7 signaling |