Coexpression cluster:C1038
From FANTOM5_SSTAR
Full id: C1038_Hepatocyte_liver_hippocampus_amygdala_caudate_corpus_thalamus
Phase1 CAGE Peaks
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 6.95890409625456e-06 | 0.00220249314646457 | 2 | 44 | Valine, leucine and isoleucine degradation (KEGG):00280 |
| 3.64966676839917e-06 | 0.00220249314646457 | 2 | 32 | Propanoate metabolism (KEGG):00640 |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0006725 | aromatic compound metabolic process | 0.00209725369783426 |
| GO:0003867 | 4-aminobutyrate transaminase activity | 0.00209725369783426 |
| GO:0019859 | thymine metabolic process | 0.00209725369783426 |
| GO:0018478 | malonate-semialdehyde dehydrogenase (acetylating) activity | 0.00209725369783426 |
| GO:0047298 | (S)-3-amino-2-methylpropionate transaminase activity | 0.00209725369783426 |
| GO:0032145 | succinate-semialdehyde dehydrogenase binding | 0.00209725369783426 |
| GO:0004491 | methylmalonate-semialdehyde dehydrogenase (acylating) activity | 0.00209725369783426 |
| GO:0032144 | 4-aminobutyrate transaminase complex | 0.00209725369783426 |
| GO:0009448 | gamma-aminobutyric acid metabolic process | 0.00209725369783426 |
| GO:0048148 | behavioral response to cocaine | 0.00209725369783426 |
| GO:0019626 | short-chain fatty acid catabolic process | 0.00209725369783426 |
| GO:0046359 | butyrate catabolic process | 0.00209725369783426 |
| GO:0006573 | valine metabolic process | 0.00209725369783426 |
| GO:0019605 | butyrate metabolic process | 0.00209725369783426 |
| GO:0016235 | aggresome | 0.00209725369783426 |
| GO:0009450 | gamma-aminobutyric acid catabolic process | 0.00209725369783426 |
| GO:0042220 | response to cocaine | 0.00279625594751804 |
| GO:0014073 | response to tropane | 0.00279625594751804 |
| GO:0046459 | short-chain fatty acid metabolic process | 0.00353200879941799 |
| GO:0009062 | fatty acid catabolic process | 0.0041941369797639 |
| GO:0048037 | cofactor binding | 0.00424254131842541 |
| GO:0016234 | inclusion body | 0.00437636192623535 |
| GO:0031018 | endocrine pancreas development | 0.00437636192623535 |
| GO:0042135 | neurotransmitter catabolic process | 0.00536802122965575 |
| GO:0043279 | response to alkaloid | 0.00536802122965575 |
| GO:0006519 | amino acid and derivative metabolic process | 0.0056332784920928 |
| GO:0046395 | carboxylic acid catabolic process | 0.00563617767666475 |
| GO:0031016 | pancreas development | 0.00563617767666475 |
| GO:0016054 | organic acid catabolic process | 0.00563617767666475 |
| GO:0042221 | response to chemical stimulus | 0.00563617767666475 |
| GO:0014070 | response to organic cyclic substance | 0.00595191720609126 |
| GO:0009308 | amine metabolic process | 0.00615585991956573 |
| GO:0006206 | pyrimidine base metabolic process | 0.00657937560058684 |
| GO:0006807 | nitrogen compound metabolic process | 0.00657937560058684 |
| GO:0042219 | amino acid derivative catabolic process | 0.00670884138064908 |
| GO:0009081 | branched chain family amino acid metabolic process | 0.00745382928836276 |
| GO:0019752 | carboxylic acid metabolic process | 0.00813738920926449 |
| GO:0006082 | organic acid metabolic process | 0.00813738920926449 |
| GO:0000062 | acyl-CoA binding | 0.00859955944077925 |
| GO:0019439 | aromatic compound catabolic process | 0.0088035397728746 |
| GO:0009112 | nucleobase metabolic process | 0.00940624816327905 |
| GO:0006629 | lipid metabolic process | 0.0103180539925961 |
| GO:0030534 | adult behavior | 0.0104316746465184 |
| GO:0044444 | cytoplasmic part | 0.0104316746465184 |
| GO:0006958 | complement activation, classical pathway | 0.0104316746465184 |
| GO:0005739 | mitochondrion | 0.0105162913588557 |
| GO:0002455 | humoral immune response mediated by circulating immunoglobulin | 0.0107005558179499 |
| GO:0005504 | fatty acid binding | 0.0108265630239047 |
| GO:0042133 | neurotransmitter metabolic process | 0.0109474069369195 |
| GO:0035270 | endocrine system development | 0.0110633973551524 |
| GO:0006956 | complement activation | 0.0125698213712117 |
| GO:0002541 | activation of plasma proteins during acute inflammatory response | 0.0125698213712117 |
| GO:0008483 | transaminase activity | 0.0145432100741649 |
| GO:0045597 | positive regulation of cell differentiation | 0.0145837638527713 |
| GO:0044242 | cellular lipid catabolic process | 0.014622825012576 |
| GO:0016620 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | 0.014959226279668 |
| GO:0016064 | immunoglobulin mediated immune response | 0.014990277895566 |
| GO:0019724 | B cell mediated immunity | 0.0150202417598716 |
| GO:0016769 | transferase activity, transferring nitrogenous groups | 0.0173066933148615 |
| GO:0010033 | response to organic substance | 0.0173066933148615 |
| GO:0048471 | perinuclear region of cytoplasm | 0.0175710701776496 |
| GO:0051094 | positive regulation of developmental process | 0.0182656147218351 |
| GO:0006220 | pyrimidine nucleotide metabolic process | 0.0182656147218351 |
| GO:0002253 | activation of immune response | 0.0182656147218351 |
| GO:0016903 | oxidoreductase activity, acting on the aldehyde or oxo group of donors | 0.0182656147218351 |
| GO:0002449 | lymphocyte mediated immunity | 0.0182656147218351 |
| GO:0006959 | humoral immune response | 0.0183675305377231 |
| GO:0002250 | adaptive immune response | 0.0183675305377231 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 0.0183675305377231 |
| GO:0002443 | leukocyte mediated immunity | 0.0183675305377231 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0183675305377231 |
| GO:0002526 | acute inflammatory response | 0.0183675305377231 |
| GO:0050778 | positive regulation of immune response | 0.0194506153245901 |
| GO:0002684 | positive regulation of immune system process | 0.0194506153245901 |
| GO:0006575 | amino acid derivative metabolic process | 0.0200815244420623 |
| GO:0050776 | regulation of immune response | 0.0215737452949274 |
| GO:0002682 | regulation of immune system process | 0.0217268489507706 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0225173967991115 |
| GO:0002252 | immune effector process | 0.0232876191353746 |
| GO:0045087 | innate immune response | 0.023829951962537 |
| GO:0030170 | pyridoxal phosphate binding | 0.0238719907821851 |
| GO:0048667 | neuron morphogenesis during differentiation | 0.0238719907821851 |
| GO:0006979 | response to oxidative stress | 0.0238719907821851 |
| GO:0048812 | neurite morphogenesis | 0.0238719907821851 |
| GO:0005737 | cytoplasm | 0.0238719907821851 |
| GO:0000904 | cellular morphogenesis during differentiation | 0.0244921440189288 |
| GO:0046483 | heterocycle metabolic process | 0.0249762716353216 |
| GO:0031175 | neurite development | 0.0256383812428713 |
| GO:0045595 | regulation of cell differentiation | 0.0270331574805088 |
| GO:0016042 | lipid catabolic process | 0.0271024798592471 |
| GO:0048666 | neuron development | 0.0282667311209228 |
| GO:0042803 | protein homodimerization activity | 0.0286823217678161 |
| GO:0006916 | anti-apoptosis | 0.030518090645957 |
| GO:0031980 | mitochondrial lumen | 0.032147883579936 |
| GO:0005759 | mitochondrial matrix | 0.032147883579936 |
| GO:0006631 | fatty acid metabolic process | 0.0331959097229849 |
| GO:0032990 | cell part morphogenesis | 0.0343677338044235 |
| GO:0048858 | cell projection morphogenesis | 0.0343677338044235 |
| GO:0030030 | cell projection organization and biogenesis | 0.0343677338044235 |
| GO:0030182 | neuron differentiation | 0.0350185658761542 |
| GO:0043066 | negative regulation of apoptosis | 0.0374598251978158 |
| GO:0043069 | negative regulation of programmed cell death | 0.0375794559595029 |
| GO:0008284 | positive regulation of cell proliferation | 0.0376966780617515 |
| GO:0050793 | regulation of developmental process | 0.0378115609926719 |
| GO:0048699 | generation of neurons | 0.0383968082218322 |
| GO:0019842 | vitamin binding | 0.0385026686984877 |
| GO:0022008 | neurogenesis | 0.0407690182779484 |
| GO:0051239 | regulation of multicellular organismal process | 0.0426851176233368 |
| GO:0032787 | monocarboxylic acid metabolic process | 0.0432231044820223 |
| GO:0050662 | coenzyme binding | 0.0432231044820223 |
| GO:0007268 | synaptic transmission | 0.0432231044820223 |
| GO:0006954 | inflammatory response | 0.0432231044820223 |
| GO:0007610 | behavior | 0.0432784217108178 |
| GO:0019899 | enzyme binding | 0.0444893924724475 |
| GO:0019226 | transmission of nerve impulse | 0.0476822767761628 |
| GO:0009117 | nucleotide metabolic process | 0.048689302116024 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.393486 |
| MA0004.1 | 0.455723 |
| MA0006.1 | 0.300178 |
| MA0007.1 | 0.437331 |
| MA0009.1 | 0.918715 |
| MA0014.1 | 0.275152 |
| MA0017.1 | 3.35603 |
| MA0019.1 | 0.602411 |
| MA0024.1 | 0.813542 |
| MA0025.1 | 1.05265 |
| MA0027.1 | 2.5321 |
| MA0028.1 | 0.315574 |
| MA0029.1 | 0.832916 |
| MA0030.1 | 0.821423 |
| MA0031.1 | 0.756713 |
| MA0038.1 | 1.3714 |
| MA0040.1 | 0.838784 |
| MA0041.1 | 0.474018 |
| MA0042.1 | 0.442535 |
| MA0043.1 | 0.919032 |
| MA0046.1 | 0.90778 |
| MA0048.1 | 0.0955945 |
| MA0050.1 | 1.12793 |
| MA0051.1 | 0.553205 |
| MA0052.1 | 0.842664 |
| MA0055.1 | 0.028436 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0912556 |
| MA0058.1 | 1.69448 |
| MA0059.1 | 0.948176 |
| MA0060.1 | 3.1469 |
| MA0061.1 | 2.9227 |
| MA0063.1 | 0 |
| MA0066.1 | 0.557833 |
| MA0067.1 | 1.23721 |
| MA0068.1 | 9.73652 |
| MA0069.1 | 0.903908 |
| MA0070.1 | 0.892666 |
| MA0071.1 | 0.518907 |
| MA0072.1 | 0.888148 |
| MA0073.1 | 1.87644 |
| MA0074.1 | 0.552456 |
| MA0076.1 | 0.377799 |
| MA0077.1 | 0.880402 |
| MA0078.1 | 2.65557 |
| MA0081.1 | 0.361233 |
| MA0083.1 | 0.926258 |
| MA0084.1 | 1.42483 |
| MA0087.1 | 0.885691 |
| MA0088.1 | 2.18672 |
| MA0089.1 | 0 |
| MA0090.1 | 0.391903 |
| MA0091.1 | 0.458301 |
| MA0092.1 | 1.07975 |
| MA0093.1 | 0.303084 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.571227 |
| MA0101.1 | 0.30624 |
| MA0103.1 | 0.291333 |
| MA0105.1 | 3.31023 |
| MA0106.1 | 0.59853 |
| MA0107.1 | 1.23931 |
| MA0108.2 | 0.753643 |
| MA0109.1 | 0 |
| MA0111.1 | 0.405141 |
| MA0113.1 | 0.614917 |
| MA0114.1 | 4.41429 |
| MA0115.1 | 1.1606 |
| MA0116.1 | 0.673701 |
| MA0117.1 | 0.956472 |
| MA0119.1 | 0.913661 |
| MA0122.1 | 0.982472 |
| MA0124.1 | 1.11898 |
| MA0125.1 | 1.0347 |
| MA0130.1 | 0 |
| MA0131.1 | 0.670358 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.949204 |
| MA0136.1 | 0.564434 |
| MA0139.1 | 0.155155 |
| MA0140.1 | 5.63072 |
| MA0141.1 | 0.359385 |
| MA0142.1 | 0.724856 |
| MA0143.1 | 0.615094 |
| MA0144.1 | 4.28036 |
| MA0145.1 | 0.0613434 |
| MA0146.1 | 0.418694 |
| MA0147.1 | 0.243042 |
| MA0148.1 | 0.480298 |
| MA0149.1 | 0.506665 |
| MA0062.2 | 0.161302 |
| MA0035.2 | 3.26158 |
| MA0039.2 | 3.00692 |
| MA0138.2 | 0.653421 |
| MA0002.2 | 0.179788 |
| MA0137.2 | 4.22944 |
| MA0104.2 | 0.189646 |
| MA0047.2 | 0.586412 |
| MA0112.2 | 4.90171 |
| MA0065.2 | 3.62396 |
| MA0150.1 | 0.386144 |
| MA0151.1 | 0 |
| MA0152.1 | 0.52279 |
| MA0153.1 | 1.01778 |
| MA0154.1 | 0.274121 |
| MA0155.1 | 0.764865 |
| MA0156.1 | 0.323987 |
| MA0157.1 | 0.697424 |
| MA0158.1 | 0 |
| MA0159.1 | 1.96124 |
| MA0160.1 | 0.495355 |
| MA0161.1 | 0 |
| MA0162.1 | 0.378102 |
| MA0163.1 | 0.0517199 |
| MA0164.1 | 0.627336 |
| MA0080.2 | 0.303167 |
| MA0018.2 | 0.599912 |
| MA0099.2 | 0.523145 |
| MA0079.2 | 1.97275 |
| MA0102.2 | 1.46209 |
| MA0258.1 | 0.209744 |
| MA0259.1 | 0.25092 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| CEBPB#1051 | 6 | 5.97836071936861 | 8.69217560109361e-05 | 0.0013016950496166 |
| EP300#2033 | 8 | 6.7739417262232 | 2.25366016107097e-07 | 1.18993940122392e-05 |
| STAT3#6774 | 6 | 7.88959874786568 | 1.7423325560997e-05 | 0.000398178270955136 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
This analysis result is provided for C0 - C305 clusters.
