Coexpression cluster:C72
From FANTOM5_SSTAR
Full id: C72_skeletal_tongue_throat_heart_diaphragm_penis_left
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 |
|---|---|---|---|---|
| 6.10106398273766e-06 | 0.00386197350107294 | 4 | 39 | Striated Muscle Contraction (Wikipathways):WP383 |
| 1.53553120835892e-05 | 0.00485995627445598 | 4 | 49 | Muscle contraction (Reactome):REACT_17044 |
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:0006936 | muscle contraction | 4.71780622765726e-13 |
| GO:0003012 | muscle system process | 4.71780622765726e-13 |
| GO:0008092 | cytoskeletal protein binding | 4.80348745343815e-10 |
| GO:0005856 | cytoskeleton | 1.10525164910753e-08 |
| GO:0043292 | contractile fiber | 1.10525164910753e-08 |
| GO:0003779 | actin binding | 1.59181340812528e-08 |
| GO:0030016 | myofibril | 1.52750872858223e-07 |
| GO:0044449 | contractile fiber part | 2.88089018463705e-07 |
| GO:0005737 | cytoplasm | 3.19969802893113e-07 |
| GO:0015629 | actin cytoskeleton | 9.28343023555808e-07 |
| GO:0006941 | striated muscle contraction | 9.60050066496648e-07 |
| GO:0043228 | non-membrane-bound organelle | 1.11647385590458e-06 |
| GO:0043232 | intracellular non-membrane-bound organelle | 1.11647385590458e-06 |
| GO:0030017 | sarcomere | 2.91006654844817e-06 |
| GO:0044444 | cytoplasmic part | 1.59373741575407e-05 |
| GO:0044430 | cytoskeletal part | 2.10350400668807e-05 |
| GO:0007517 | muscle development | 7.39952479970909e-05 |
| GO:0005515 | protein binding | 0.000123889876503251 |
| GO:0032501 | multicellular organismal process | 0.000132708827171224 |
| GO:0005626 | insoluble fraction | 0.000348801263931253 |
| GO:0005523 | tropomyosin binding | 0.00038696732543958 |
| GO:0051393 | alpha-actinin binding | 0.000415003140747196 |
| GO:0003008 | system process | 0.000562331685675669 |
| GO:0000267 | cell fraction | 0.000574835885879634 |
| GO:0042805 | actinin binding | 0.00121400091885135 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.00164998697279683 |
| GO:0004115 | 3',5'-cyclic-AMP phosphodiesterase activity | 0.00219001172961378 |
| GO:0015270 | dihydropyridine-sensitive calcium channel activity | 0.00219001172961378 |
| GO:0044424 | intracellular part | 0.00219001172961378 |
| GO:0022836 | gated channel activity | 0.00219001172961378 |
| GO:0008307 | structural constituent of muscle | 0.00219001172961378 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.00219001172961378 |
| GO:0015630 | microtubule cytoskeleton | 0.00237390257288476 |
| GO:0051261 | protein depolymerization | 0.00255112441499983 |
| GO:0030832 | regulation of actin filament length | 0.00255112441499983 |
| GO:0032535 | regulation of cellular component size | 0.00257385019430711 |
| GO:0032956 | regulation of actin cytoskeleton organization and biogenesis | 0.00257385019430711 |
| GO:0005813 | centrosome | 0.00302637363172356 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.00322034012142042 |
| GO:0051129 | negative regulation of cellular component organization and biogenesis | 0.00322034012142042 |
| GO:0043687 | post-translational protein modification | 0.00364982554883671 |
| GO:0030029 | actin filament-based process | 0.00364982554883671 |
| GO:0033043 | regulation of organelle organization and biogenesis | 0.00364982554883671 |
| GO:0051493 | regulation of cytoskeleton organization and biogenesis | 0.00364982554883671 |
| GO:0043412 | biopolymer modification | 0.00397619239306852 |
| GO:0005261 | cation channel activity | 0.0040325499629083 |
| GO:0005815 | microtubule organizing center | 0.0040325499629083 |
| GO:0005790 | smooth endoplasmic reticulum | 0.00413319883702199 |
| GO:0030018 | Z disc | 0.00545874206205575 |
| GO:0007519 | skeletal muscle development | 0.00545874206205575 |
| GO:0043229 | intracellular organelle | 0.00667615324188191 |
| GO:0032982 | myosin filament | 0.00667615324188191 |
| GO:0005863 | striated muscle thick filament | 0.00667615324188191 |
| GO:0043226 | organelle | 0.00667615324188191 |
| GO:0031674 | I band | 0.00729955721247181 |
| GO:0005216 | ion channel activity | 0.00729955721247181 |
| GO:0005624 | membrane fraction | 0.00729955721247181 |
| GO:0022832 | voltage-gated channel activity | 0.00729955721247181 |
| GO:0005244 | voltage-gated ion channel activity | 0.00729955721247181 |
| GO:0022838 | substrate specific channel activity | 0.00738676379197793 |
| GO:0046873 | metal ion transmembrane transporter activity | 0.00757041830826794 |
| GO:0022803 | passive transmembrane transporter activity | 0.00759204471381507 |
| GO:0015267 | channel activity | 0.00759204471381507 |
| GO:0006464 | protein modification process | 0.00761312902011161 |
| GO:0014706 | striated muscle development | 0.00923653099126956 |
| GO:0051693 | actin filament capping | 0.00923653099126956 |
| GO:0051016 | barbed-end actin filament capping | 0.00923653099126956 |
| GO:0065008 | regulation of biological quality | 0.00923653099126956 |
| GO:0030835 | negative regulation of actin filament depolymerization | 0.00978453731110029 |
| GO:0005248 | voltage-gated sodium channel activity | 0.00978453731110029 |
| GO:0030834 | regulation of actin filament depolymerization | 0.0102162713259087 |
| GO:0030042 | actin filament depolymerization | 0.0102162713259087 |
| GO:0043161 | proteasomal ubiquitin-dependent protein catabolic process | 0.0102162713259087 |
| GO:0006512 | ubiquitin cycle | 0.0102162713259087 |
| GO:0005859 | muscle myosin complex | 0.0115045985346233 |
| GO:0016528 | sarcoplasm | 0.0115045985346233 |
| GO:0016529 | sarcoplasmic reticulum | 0.0115045985346233 |
| GO:0016460 | myosin II complex | 0.0122866854236638 |
| GO:0051248 | negative regulation of protein metabolic process | 0.0124175603495476 |
| GO:0044446 | intracellular organelle part | 0.0131669436439726 |
| GO:0044422 | organelle part | 0.0135033263070627 |
| GO:0043234 | protein complex | 0.014746835800996 |
| GO:0005262 | calcium channel activity | 0.0168001239796566 |
| GO:0031432 | titin binding | 0.0168001239796566 |
| GO:0005130 | granulocyte colony-stimulating factor receptor binding | 0.0168001239796566 |
| GO:0015755 | fructose transport | 0.0168001239796566 |
| GO:0022843 | voltage-gated cation channel activity | 0.0168001239796566 |
| GO:0005622 | intracellular | 0.0168001239796566 |
| GO:0006811 | ion transport | 0.0178833616688749 |
| GO:0009892 | negative regulation of metabolic process | 0.017984009377158 |
| GO:0008324 | cation transmembrane transporter activity | 0.0186624188117122 |
| GO:0048523 | negative regulation of cellular process | 0.0206785466930507 |
| GO:0005891 | voltage-gated calcium channel complex | 0.0206785466930507 |
| GO:0048513 | organ development | 0.0206785466930507 |
| GO:0051015 | actin filament binding | 0.0225951056945113 |
| GO:0005516 | calmodulin binding | 0.0242672502478497 |
| GO:0048519 | negative regulation of biological process | 0.0248333300298026 |
| GO:0008064 | regulation of actin polymerization and/or depolymerization | 0.0277726489503542 |
| GO:0004114 | 3',5'-cyclic-nucleotide phosphodiesterase activity | 0.028561141721818 |
| GO:0005927 | muscle tendon junction | 0.028561141721818 |
| GO:0008184 | glycogen phosphorylase activity | 0.028561141721818 |
| GO:0051371 | muscle alpha-actinin binding | 0.028561141721818 |
| GO:0005977 | glycogen metabolic process | 0.0297827758821279 |
| GO:0004112 | cyclic-nucleotide phosphodiesterase activity | 0.0297827758821279 |
| GO:0006073 | glucan metabolic process | 0.0307397024964582 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.0308174718294037 |
| GO:0006996 | organelle organization and biogenesis | 0.031183611676447 |
| GO:0006112 | energy reserve metabolic process | 0.0389703584237744 |
| GO:0005218 | intracellular ligand-gated calcium channel activity | 0.0393269337737831 |
| GO:0005353 | fructose transmembrane transporter activity | 0.0393269337737831 |
| GO:0005219 | ryanodine-sensitive calcium-release channel activity | 0.0393269337737831 |
| GO:0005272 | sodium channel activity | 0.0402774717560184 |
| GO:0015075 | ion transmembrane transporter activity | 0.0411999819333484 |
| GO:0006816 | calcium ion transport | 0.0416278925607318 |
| GO:0019992 | diacylglycerol binding | 0.0416278925607318 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0416278925607318 |
| GO:0008154 | actin polymerization and/or depolymerization | 0.0434972830287973 |
| GO:0042578 | phosphoric ester hydrolase activity | 0.0434972830287973 |
| GO:0022857 | transmembrane transporter activity | 0.0434972830287973 |
| GO:0008138 | protein tyrosine/serine/threonine phosphatase activity | 0.0443840293604972 |
| GO:0033018 | sarcoplasmic reticulum lumen | 0.0443840293604972 |
| GO:0032364 | oxygen homeostasis | 0.0443840293604972 |
| GO:0001892 | embryonic placenta development | 0.0443840293604972 |
| GO:0033483 | gas homeostasis | 0.0443840293604972 |
| GO:0006110 | regulation of glycolysis | 0.0443840293604972 |
| GO:0005315 | inorganic phosphate transmembrane transporter activity | 0.0443840293604972 |
| GO:0005955 | calcineurin complex | 0.0443840293604972 |
| GO:0030851 | granulocyte differentiation | 0.0443840293604972 |
| GO:0007525 | somatic muscle development | 0.0443840293604972 |
| GO:0043034 | costamere | 0.0443840293604972 |
| GO:0016068 | type I hypersensitivity | 0.0443840293604972 |
| GO:0005245 | voltage-gated calcium channel activity | 0.0467031129380266 |
| GO:0006812 | cation transport | 0.0478529649024454 |
| GO:0048856 | anatomical structure development | 0.0486770779119948 |
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) |
|---|---|
|
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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
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