Coexpression cluster:C56
From FANTOM5_SSTAR
Full id: C56_heart_left_umbilical_skeletal_penis_diaphragm_tongue
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 |
|---|---|---|---|---|
| 6.1282881663948e-05 | 0.00775841281865581 | 5 | 177 | Calcium signaling pathway (KEGG):04020 |
| 3.29661271431625e-05 | 0.00695585282720729 | 4 | 77 | Cardiac muscle contraction (KEGG):04260 |
| 4.42943345639642e-05 | 0.00700957844474733 | 4 | 83 | Hypertrophic cardiomyopathy (HCM) (KEGG):05410 |
| 2.8178069949548e-05 | 0.00695585282720729 | 4 | 74 | Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412 |
| 2.3046604318716e-06 | 0.00145885005337472 | 5 | 90 | Dilated cardiomyopathy (KEGG):05414 |
| 0.000152771703903162 | 0.0161174147617836 | 3 | 44 | Heart Development (Wikipathways):WP1591 |
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:0005856 | cytoskeleton | 3.02581251423143e-06 |
| GO:0015629 | actin cytoskeleton | 1.77735874149302e-05 |
| GO:0005515 | protein binding | 1.77735874149302e-05 |
| GO:0003779 | actin binding | 0.000226266958611217 |
| GO:0008092 | cytoskeletal protein binding | 0.000226266958611217 |
| GO:0005737 | cytoplasm | 0.000226266958611217 |
| GO:0043228 | non-membrane-bound organelle | 0.00048660186084386 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.00048660186084386 |
| GO:0006936 | muscle contraction | 0.000972444371781958 |
| GO:0003012 | muscle system process | 0.000972444371781958 |
| GO:0042805 | actinin binding | 0.00209396948690234 |
| GO:0048513 | organ development | 0.00246493934239045 |
| GO:0014855 | striated muscle cell proliferation | 0.00246493934239045 |
| GO:0060038 | cardiac muscle cell proliferation | 0.00246493934239045 |
| GO:0051179 | localization | 0.00665445545063212 |
| GO:0032501 | multicellular organismal process | 0.00736201752690342 |
| GO:0044456 | synapse part | 0.00935431459775382 |
| GO:0005913 | cell-cell adherens junction | 0.00988614168572277 |
| GO:0007517 | muscle development | 0.0107637275306919 |
| GO:0016043 | cellular component organization and biogenesis | 0.0109570320212676 |
| GO:0006816 | calcium ion transport | 0.0123170982480961 |
| GO:0030336 | negative regulation of cell migration | 0.0170127041511421 |
| GO:0014706 | striated muscle development | 0.0170127041511421 |
| GO:0033002 | muscle cell proliferation | 0.0170127041511421 |
| GO:0051234 | establishment of localization | 0.0170127041511421 |
| GO:0043229 | intracellular organelle | 0.0170127041511421 |
| GO:0043226 | organelle | 0.0170127041511421 |
| GO:0048731 | system development | 0.0170127041511421 |
| GO:0007507 | heart development | 0.0170127041511421 |
| GO:0051271 | negative regulation of cell motility | 0.0190113139170204 |
| GO:0044459 | plasma membrane part | 0.0194201755717319 |
| GO:0040013 | negative regulation of locomotion | 0.0194201755717319 |
| GO:0016528 | sarcoplasm | 0.0198434707110117 |
| GO:0016529 | sarcoplasmic reticulum | 0.0198434707110117 |
| GO:0048856 | anatomical structure development | 0.0206083221838369 |
| GO:0051049 | regulation of transport | 0.0214231971388989 |
| GO:0015674 | di-, tri-valent inorganic cation transport | 0.0214231971388989 |
| GO:0044464 | cell part | 0.0245403105290486 |
| GO:0030029 | actin filament-based process | 0.0245403105290486 |
| GO:0044430 | cytoskeletal part | 0.0260786360870696 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.0269489767543233 |
| GO:0006810 | transport | 0.0269489767543233 |
| GO:0033612 | receptor serine/threonine kinase binding | 0.0269489767543233 |
| GO:0004231 | insulysin activity | 0.0269489767543233 |
| GO:0060044 | negative regulation of cardiac muscle cell proliferation | 0.0269489767543233 |
| GO:0060039 | pericardium development | 0.0269489767543233 |
| GO:0008613 | diuretic hormone activity | 0.0269489767543233 |
| GO:0032502 | developmental process | 0.0285060976477417 |
| GO:0003008 | system process | 0.0285060976477417 |
| GO:0005891 | voltage-gated calcium channel complex | 0.029529748298574 |
| GO:0008283 | cell proliferation | 0.0343463216863682 |
| GO:0045211 | postsynaptic membrane | 0.0355730679489877 |
| GO:0044424 | intracellular part | 0.0372190023142243 |
| GO:0008015 | blood circulation | 0.0372190023142243 |
| GO:0003013 | circulatory system process | 0.0372190023142243 |
| GO:0045121 | lipid raft | 0.0372190023142243 |
| GO:0016316 | phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity | 0.0372190023142243 |
| GO:0042030 | ATPase inhibitor activity | 0.0372190023142243 |
| GO:0005915 | zonula adherens | 0.0372190023142243 |
| GO:0031014 | troponin T binding | 0.0372190023142243 |
| GO:0060043 | regulation of cardiac muscle cell proliferation | 0.0372190023142243 |
| GO:0032387 | negative regulation of intracellular transport | 0.0372190023142243 |
| GO:0051890 | regulation of cardioblast differentiation | 0.0372190023142243 |
| GO:0016080 | synaptic vesicle targeting | 0.0372190023142243 |
| GO:0051891 | positive regulation of cardioblast differentiation | 0.0372190023142243 |
| GO:0051371 | muscle alpha-actinin binding | 0.0372190023142243 |
| GO:0031013 | troponin I binding | 0.0372190023142243 |
| GO:0007206 | metabotropic glutamate receptor, phospholipase C activating pathway | 0.0372190023142243 |
| GO:0051649 | establishment of cellular localization | 0.0409939404348144 |
| GO:0030016 | myofibril | 0.0422151618077535 |
| GO:0030308 | negative regulation of cell growth | 0.0422151618077535 |
| GO:0005912 | adherens junction | 0.0425870509854035 |
| GO:0045792 | negative regulation of cell size | 0.0425870509854035 |
| GO:0008217 | regulation of blood pressure | 0.0432258510182351 |
| GO:0051641 | cellular localization | 0.0432258510182351 |
| GO:0007154 | cell communication | 0.0433862427113786 |
| GO:0005509 | calcium ion binding | 0.0433862427113786 |
| GO:0051393 | alpha-actinin binding | 0.0433862427113786 |
| GO:0043114 | regulation of vascular permeability | 0.0433862427113786 |
| GO:0045822 | negative regulation of heart contraction | 0.0433862427113786 |
| GO:0003875 | ADP-ribosylarginine hydrolase activity | 0.0433862427113786 |
| GO:0004802 | transketolase activity | 0.0433862427113786 |
| GO:0035117 | embryonic arm morphogenesis | 0.0433862427113786 |
| GO:0035140 | arm morphogenesis | 0.0433862427113786 |
| GO:0006772 | thiamin metabolic process | 0.0433862427113786 |
| GO:0051725 | protein amino acid de-ADP-ribosylation | 0.0433862427113786 |
| GO:0030334 | regulation of cell migration | 0.0433862427113786 |
| GO:0044449 | contractile fiber part | 0.0433862427113786 |
| GO:0045926 | negative regulation of growth | 0.0439877529669852 |
| GO:0005622 | intracellular | 0.0439877529669852 |
| GO:0048519 | negative regulation of biological process | 0.0462025731642965 |
| GO:0043292 | contractile fiber | 0.0470434621559895 |
| GO:0007267 | cell-cell signaling | 0.0490539250625145 |
| GO:0046907 | intracellular transport | 0.0490539250625145 |
| GO:0007519 | skeletal muscle development | 0.0490539250625145 |
| GO:0005245 | voltage-gated calcium channel activity | 0.0490539250625145 |
| GO:0051270 | regulation of cell motility | 0.0490539250625145 |
| GO:0010002 | cardioblast differentiation | 0.0490539250625145 |
| GO:0006110 | regulation of glycolysis | 0.0490539250625145 |
| GO:0007262 | STAT protein nuclear translocation | 0.0490539250625145 |
| GO:0030147 | natriuresis | 0.0490539250625145 |
| GO:0043034 | costamere | 0.0490539250625145 |
| GO:0016068 | type I hypersensitivity | 0.0490539250625145 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| heart disease | 8.50e-50 | 2 |
| vascular disease | 1.26e-25 | 1 |
| ischemia | 1.26e-25 | 1 |
| extrinsic cardiomyopathy | 1.26e-25 | 1 |
| myocardial ischemia | 1.26e-25 | 1 |
| myocardial infarction | 1.26e-25 | 1 |
| cardiovascular system disease | 1.62e-25 | 4 |
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) |
|---|---|
|
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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
No analysis results for this cluster
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
