Coexpression cluster:C59
From FANTOM5_SSTAR
Full id: C59_Smooth_Fibroblast_Mesenchymal_tenocyte_Ewing_skin_hepatic
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 |
|---|---|---|---|---|
| 0.000481694892022353 | 0.030491286665015 | 2 | 200 | Focal adhesion (KEGG):04510 |
| 8.71154780629587e-05 | 0.00919068293564215 | 2 | 85 | ECM-receptor interaction (KEGG):04512 |
| 7.90849808217909e-05 | 0.00919068293564215 | 2 | 81 | Protein digestion and absorption (KEGG):04974 |
| 0.000135597657293231 | 0.0107291646333269 | 2 | 106 | Amoebiasis (KEGG):05146 |
| 0.000425848206009 | 0.029951323822633 | 2 | 188 | Focal Adhesion (Wikipathways):WP306 |
| 1.13900315595625e-05 | 0.00720988997720308 | 2 | 31 | Inflammatory Response Pathway (Wikipathways):WP453 |
| 0.000120663279167051 | 0.0107291646333269 | 2 | 100 | Senescence and Autophagy (Wikipathways):WP615 |
| 8.71154780629587e-05 | 0.00919068293564215 | 2 | 85 | Integrin cell surface interactions (Reactome):REACT_13552 |
| 4.21831510575296e-05 | 0.00919068293564215 | 3 | 466 | Hemostasis (Reactome):REACT_604 |
| 5.08276270087817e-05 | 0.00919068293564215 | 2 | 65 | Signaling by PDGF (Reactome):REACT_16888 |
| 0.000842854829985519 | 0.0485024643073485 | 2 | 265 | Axon guidance (Reactome):REACT_18266 |
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:0005584 | collagen type I | 6.44603038489087e-06 |
| GO:0008147 | structural constituent of bone | 6.44603038489087e-06 |
| GO:0044420 | extracellular matrix part | 2.30314774701338e-05 |
| GO:0005583 | fibrillar collagen | 2.9532131139368e-05 |
| GO:0001501 | skeletal development | 5.17325564363905e-05 |
| GO:0044421 | extracellular region part | 5.17325564363905e-05 |
| GO:0005578 | proteinaceous extracellular matrix | 0.000328619286134617 |
| GO:0005581 | collagen | 0.00038321432857395 |
| GO:0031214 | biomineral formation | 0.000818453034055813 |
| GO:0001503 | ossification | 0.000818453034055813 |
| GO:0046849 | bone remodeling | 0.000885909097236298 |
| GO:0048771 | tissue remodeling | 0.000971847088610543 |
| GO:0005201 | extracellular matrix structural constituent | 0.00122918978539034 |
| GO:0050954 | sensory perception of mechanical stimulus | 0.00122918978539034 |
| GO:0007605 | sensory perception of sound | 0.00122918978539034 |
| GO:0006817 | phosphate transport | 0.00135234513845316 |
| GO:0048513 | organ development | 0.00258796641079435 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.00258796641079435 |
| GO:0015698 | inorganic anion transport | 0.00375061241749324 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.00465995155994494 |
| GO:0009888 | tissue development | 0.00465995155994494 |
| GO:0006820 | anion transport | 0.00498425912105211 |
| GO:0048731 | system development | 0.00528130714890037 |
| GO:0007159 | leukocyte adhesion | 0.00760027328706414 |
| GO:0051591 | response to cAMP | 0.00802541607704151 |
| GO:0048856 | anatomical structure development | 0.00878098692929916 |
| GO:0031960 | response to corticosteroid stimulus | 0.00878098692929916 |
| GO:0009103 | lipopolysaccharide biosynthetic process | 0.00911818034281925 |
| GO:0008653 | lipopolysaccharide metabolic process | 0.00943204502218036 |
| GO:0009612 | response to mechanical stimulus | 0.0103321126366538 |
| GO:0007275 | multicellular organismal development | 0.0108246521555363 |
| GO:0005518 | collagen binding | 0.0108246521555363 |
| GO:0042542 | response to hydrogen peroxide | 0.0110484362287232 |
| GO:0043434 | response to peptide hormone stimulus | 0.0117944415559125 |
| GO:0000302 | response to reactive oxygen species | 0.0140572863723272 |
| GO:0048545 | response to steroid hormone stimulus | 0.0187175629731496 |
| GO:0033692 | cellular polysaccharide biosynthetic process | 0.0191166387066115 |
| GO:0000271 | polysaccharide biosynthetic process | 0.0191166387066115 |
| GO:0007584 | response to nutrient | 0.0191166387066115 |
| GO:0010035 | response to inorganic substance | 0.0191166387066115 |
| GO:0007600 | sensory perception | 0.0223351177534285 |
| GO:0032502 | developmental process | 0.0242096134401782 |
| GO:0031667 | response to nutrient levels | 0.0253772630408364 |
| GO:0010033 | response to organic substance | 0.0256241731877004 |
| GO:0005788 | endoplasmic reticulum lumen | 0.0258599195614814 |
| GO:0009991 | response to extracellular stimulus | 0.0260852302672223 |
| GO:0005604 | basement membrane | 0.0281819078697815 |
| GO:0009725 | response to hormone stimulus | 0.0281819078697815 |
| GO:0008201 | heparin binding | 0.0281819078697815 |
| GO:0032501 | multicellular organismal process | 0.0296067134600146 |
| GO:0044264 | cellular polysaccharide metabolic process | 0.0299128253104611 |
| GO:0005976 | polysaccharide metabolic process | 0.0300325558884176 |
| GO:0050877 | neurological system process | 0.0302549691748208 |
| GO:0043284 | biopolymer biosynthetic process | 0.0334936724509308 |
| GO:0006811 | ion transport | 0.0334936724509308 |
| GO:0005539 | glycosaminoglycan binding | 0.0356195299440271 |
| GO:0005509 | calcium ion binding | 0.0359449920463006 |
| GO:0030247 | polysaccharide binding | 0.0359449920463006 |
| GO:0005507 | copper ion binding | 0.0359449920463006 |
| GO:0006979 | response to oxidative stress | 0.0362458117056837 |
| GO:0001871 | pattern binding | 0.0368382240892378 |
| GO:0051179 | localization | 0.0368382240892378 |
| GO:0003008 | system process | 0.0368382240892378 |
| GO:0005515 | protein binding | 0.0376066553049762 |
| GO:0008544 | epidermis development | 0.0376066553049762 |
| GO:0016051 | carbohydrate biosynthetic process | 0.0378532123607544 |
| GO:0007398 | ectoderm development | 0.0394312995832476 |
| GO:0009628 | response to abiotic stimulus | 0.0438583468469463 |
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>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| fibroblast | 3.35e-28 | 76 |
| contractile cell | 8.61e-21 | 59 |
| muscle precursor cell | 4.09e-20 | 58 |
| myoblast | 4.09e-20 | 58 |
| multi-potent skeletal muscle stem cell | 4.09e-20 | 58 |
| muscle cell | 3.20e-19 | 55 |
| non-terminally differentiated cell | 7.62e-17 | 106 |
| multi fate stem cell | 8.29e-17 | 427 |
| smooth muscle cell | 5.98e-16 | 43 |
| smooth muscle myoblast | 5.98e-16 | 43 |
| somatic stem cell | 9.89e-16 | 433 |
| electrically responsive cell | 1.67e-15 | 61 |
| electrically active cell | 1.67e-15 | 61 |
| stem cell | 1.18e-14 | 441 |
| vascular associated smooth muscle cell | 2.28e-11 | 32 |
| somatic cell | 2.97e-09 | 588 |
| skin fibroblast | 3.45e-09 | 23 |
| preadipocyte | 9.58e-09 | 12 |
| cardiocyte | 6.91e-08 | 16 |
| connective tissue cell | 1.17e-07 | 361 |
| mesodermal cell | 1.39e-07 | 121 |
| stromal cell | 3.97e-07 | 28 |
| extraembryonic cell | 5.06e-07 | 19 |
| extracellular matrix secreting cell | 5.52e-07 | 15 |
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
