Coexpression cluster:C125
From FANTOM5_SSTAR
Full id: C125_mucinous_alveolar_mesothelioma_Smooth_lung_CD14_Nucleus
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 |
|---|---|---|---|---|
| 3.08879411926494e-05 | 0.00977603338747354 | 2 | 9 | Benzo(a)pyrene metabolism (Wikipathways):WP696 |
| 2.14511302572539e-05 | 0.00977603338747354 | 4 | 175 | metapathway biotransformation (Wikipathways):WP702 |
| 0.000178921968614274 | 0.0377525353776118 | 2 | 21 | {POU2F1,21} (Static Module):NA |
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:0047026 | 3-alpha-hydroxysteroid dehydrogenase (A-specific) activity | 0.000196426050335292 |
| GO:0047115 | trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity | 0.000294517646387335 |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 0.000495130272441399 |
| GO:0016614 | oxidoreductase activity, acting on CH-OH group of donors | 0.000495130272441399 |
| GO:0004033 | aldo-keto reductase activity | 0.00258215931067551 |
| GO:0016628 | oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor | 0.00331866359094554 |
| GO:0006693 | prostaglandin metabolic process | 0.00331866359094554 |
| GO:0006692 | prostanoid metabolic process | 0.00331866359094554 |
| GO:0005737 | cytoplasm | 0.00908720129811135 |
| GO:0016229 | steroid dehydrogenase activity | 0.00962304248041086 |
| GO:0044265 | cellular macromolecule catabolic process | 0.0158728621380326 |
| GO:0006690 | icosanoid metabolic process | 0.0196592456954908 |
| GO:0047017 | prostaglandin-F synthase activity | 0.0233314313144762 |
| GO:0009057 | macromolecule catabolic process | 0.0243425548611502 |
| GO:0032052 | bile acid binding | 0.0384079954882468 |
| GO:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | 0.0384079954882468 |
| GO:0008283 | cell proliferation | 0.0384079954882468 |
| GO:0007586 | digestion | 0.0395363767192471 |
| GO:0044248 | cellular catabolic process | 0.0395363767192471 |
| GO:0042808 | neuronal Cdc2-like kinase binding | 0.0395363767192471 |
| GO:0030297 | transmembrane receptor protein tyrosine kinase activator activity | 0.0395363767192471 |
| GO:0047045 | testosterone 17-beta-dehydrogenase (NADP+) activity | 0.0395363767192471 |
| GO:0047756 | chondroitin 4-sulfotransferase activity | 0.0395363767192471 |
| GO:0032501 | multicellular organismal process | 0.046617552219066 |
| GO:0050327 | testosterone 17-beta-dehydrogenase activity | 0.046617552219066 |
| GO:0030971 | receptor tyrosine kinase binding | 0.046617552219066 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| animal cell | 8.22e-23 | 679 |
| eukaryotic cell | 8.22e-23 | 679 |
| native cell | 3.13e-16 | 722 |
| non-terminally differentiated cell | 8.41e-10 | 180 |
| classical monocyte | 4.35e-09 | 45 |
| fibroblast | 6.50e-09 | 75 |
| multi fate stem cell | 1.93e-08 | 430 |
| monopoietic cell | 2.13e-08 | 63 |
| monocyte | 2.13e-08 | 63 |
| monoblast | 2.13e-08 | 63 |
| promonocyte | 2.13e-08 | 63 |
| somatic cell | 2.88e-08 | 591 |
| CD14-positive, CD16-negative classical monocyte | 6.88e-08 | 42 |
| somatic stem cell | 8.84e-08 | 436 |
| macrophage dendritic cell progenitor | 1.63e-07 | 65 |
| myeloid lineage restricted progenitor cell | 2.01e-07 | 70 |
| stem cell | 6.73e-07 | 444 |
| mesothelial cell | 9.63e-07 | 19 |
| Ontology term | p-value | n |
|---|---|---|
| mesoderm | 9.86e-12 | 448 |
| mesoderm-derived structure | 9.86e-12 | 448 |
| presumptive mesoderm | 9.86e-12 | 448 |
| musculoskeletal system | 6.72e-09 | 167 |
| multi-cellular organism | 3.82e-07 | 659 |
| bone marrow | 4.37e-07 | 80 |
| Ontology term | p-value | n |
|---|---|---|
| carcinoma | 1.16e-10 | 106 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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 | 46 | 2.58220275202776 | 5.9558087765293e-10 | 5.71183391011886e-08 |
| EP300#2033 | 49 | 2.33748693369674 | 3.79787354777007e-09 | 3.11583751339795e-07 |
| FOS#2353 | 38 | 2.40790353336611 | 1.9390957584687e-07 | 1.05477719749329e-05 |
| FOSL1#8061 | 11 | 3.07640406253594 | 0.000997151674183716 | 0.0071491400906208 |
| FOSL2#2355 | 16 | 1.90762823713371 | 0.00997744027680398 | 0.037426689356696 |
| JUN#3725 | 33 | 2.90791100948661 | 2.03666225375693e-08 | 1.45093430504856e-06 |
| JUNB#3726 | 13 | 2.80238186322306 | 0.000824549589131977 | 0.00627524116733619 |
| JUND#3727 | 54 | 2.65994262578194 | 2.55805097394752e-12 | 3.44722949249168e-10 |
| MAFF#23764 | 15 | 5.94880526302238 | 4.40808559252356e-08 | 2.88999404392698e-06 |
| MAFK#7975 | 36 | 6.87060840113998 | 3.18013373121331e-20 | 8.18054154566962e-18 |
| NFE2#4778 | 17 | 9.24276359913869 | 6.73642927467144e-12 | 8.59030448128707e-10 |
| NR3C1#2908 | 40 | 4.21775305103466 | 3.38099307939824e-15 | 6.04636192156288e-13 |
| STAT3#6774 | 35 | 2.59282587958027 | 1.17357416348617e-07 | 6.77165260001836e-06 |
| TFAP2C#7022 | 22 | 1.67466922124595 | 0.0114525610452804 | 0.04189911454822 |
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
