Coexpression cluster:C318
From FANTOM5_SSTAR
Full id: C318_hepatoma_Intestinal_bile_small_colon_Prostate_endometrial
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 |
|---|---|---|---|---|
| 6.26588234213711e-05 | 0.0287703396869713 | 2 | 59 | Arachidonic acid metabolism (KEGG):00590 |
| 9.0901547194222e-05 | 0.0287703396869713 | 2 | 71 | Metabolism of xenobiotics by cytochrome P450 (KEGG):00980 |
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:0047017 | prostaglandin-F synthase activity | 0.00874172177855952 |
| GO:0047026 | 3-alpha-hydroxysteroid dehydrogenase (A-specific) activity | 0.00874172177855952 |
| GO:0047045 | testosterone 17-beta-dehydrogenase (NADP+) activity | 0.00874172177855952 |
| GO:0047115 | trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity | 0.00874172177855952 |
| GO:0050327 | testosterone 17-beta-dehydrogenase activity | 0.0093240915001036 |
| GO:0005577 | fibrinogen complex | 0.0165019362595048 |
| GO:0004033 | aldo-keto reductase activity | 0.0165019362595048 |
| GO:0015804 | neutral amino acid transport | 0.0165019362595048 |
| GO:0016628 | oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor | 0.0165019362595048 |
| GO:0006693 | prostaglandin metabolic process | 0.0165019362595048 |
| GO:0006692 | prostanoid metabolic process | 0.0165019362595048 |
| GO:0015175 | neutral amino acid transmembrane transporter activity | 0.0165019362595048 |
| GO:0006118 | electron transport | 0.0201970832734816 |
| GO:0050381 | unspecific monooxygenase activity | 0.0216241942435844 |
| GO:0016229 | steroid dehydrogenase activity | 0.024833518960349 |
| GO:0006091 | generation of precursor metabolites and energy | 0.0272454932255383 |
| GO:0016712 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 0.0306091097628793 |
| GO:0006690 | icosanoid metabolic process | 0.0306091097628793 |
| GO:0005328 | neurotransmitter:sodium symporter activity | 0.0306091097628793 |
| GO:0005326 | neurotransmitter transporter activity | 0.0308192896656132 |
| GO:0015171 | amino acid transmembrane transporter activity | 0.034874355006795 |
| GO:0006865 | amino acid transport | 0.0369765176591999 |
| GO:0006836 | neurotransmitter transport | 0.037764746818911 |
| GO:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | 0.037764746818911 |
| GO:0015837 | amine transport | 0.037764746818911 |
| GO:0015370 | solute:sodium symporter activity | 0.037764746818911 |
| GO:0046943 | carboxylic acid transmembrane transporter activity | 0.037764746818911 |
| GO:0046942 | carboxylic acid transport | 0.037764746818911 |
| GO:0015849 | organic acid transport | 0.037764746818911 |
| GO:0005342 | organic acid transmembrane transporter activity | 0.037764746818911 |
| GO:0016491 | oxidoreductase activity | 0.037764746818911 |
| GO:0015294 | solute:cation symporter activity | 0.0413201004265023 |
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 |
|---|---|---|
| epithelial cell of prostate | 1.12e-17 | 3 |
| intestinal epithelial cell | 1.13e-13 | 4 |
| endodermal cell | 1.42e-08 | 58 |
| Ontology term | p-value | n |
|---|---|---|
| gallbladder | 8.00e-18 | 3 |
| gall bladder primordium | 8.00e-18 | 3 |
| gut epithelium | 1.70e-15 | 54 |
| intestinal mucosa | 1.13e-13 | 4 |
| wall of intestine | 1.13e-13 | 4 |
| gastrointestinal system mucosa | 1.13e-13 | 4 |
| gastrointestinal system epithelium | 1.13e-13 | 4 |
| intestinal epithelium | 1.13e-13 | 4 |
| endo-epithelium | 1.66e-10 | 82 |
| epithelium of foregut-midgut junction | 5.06e-09 | 25 |
| anatomical boundary | 5.06e-09 | 25 |
| hepatobiliary system | 5.06e-09 | 25 |
| foregut-midgut junction | 5.06e-09 | 25 |
| septum transversum | 5.06e-09 | 25 |
| epithelium of mucosa | 1.69e-07 | 8 |
| biliary system | 7.91e-07 | 9 |
| biliary tree | 7.91e-07 | 9 |
| biliary bud | 7.91e-07 | 9 |
| simple columnar epithelium | 8.37e-07 | 9 |
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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| FOXA2#3170 | 6 | 3.99412925718896 | 0.00351570543637029 | 0.0178509776882238 |
| MAFF#23764 | 4 | 6.08814664756164 | 0.00410937478105608 | 0.0195864819623364 |
| MAFK#7975 | 5 | 3.66226123484188 | 0.0111349017815124 | 0.040943492136724 |
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.
