Coexpression cluster:C190
From FANTOM5_SSTAR
Full id: C190_colon_small_rectum_duodenum_appendix_temporal_oral
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 |
|---|---|---|---|---|
| 1.89711789408108e-05 | 0.0120087562695332 | 6 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
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:0016021 | integral to membrane | 0.0208338023654932 |
| GO:0031224 | intrinsic to membrane | 0.0208338023654932 |
| GO:0044425 | membrane part | 0.0285712177267866 |
| GO:0022804 | active transmembrane transporter activity | 0.0338759110886178 |
| GO:0005886 | plasma membrane | 0.0338759110886178 |
| GO:0006937 | regulation of muscle contraction | 0.0338759110886178 |
| GO:0022857 | transmembrane transporter activity | 0.0338759110886178 |
| GO:0015361 | low affinity sodium:dicarboxylate symporter activity | 0.0338759110886178 |
| GO:0001665 | alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity | 0.0338759110886178 |
| GO:0001977 | renal regulation of blood volume | 0.0338759110886178 |
| GO:0002017 | aldosterone mediated regulation of blood volume | 0.0338759110886178 |
| GO:0003845 | 11-beta-hydroxysteroid dehydrogenase activity | 0.0338759110886178 |
| GO:0022892 | substrate-specific transporter activity | 0.0338759110886178 |
| GO:0015075 | ion transmembrane transporter activity | 0.0338759110886178 |
| GO:0005774 | vacuolar membrane | 0.0338759110886178 |
| GO:0044437 | vacuolar part | 0.0338759110886178 |
| GO:0032328 | alanine transport | 0.0338759110886178 |
| GO:0001618 | viral receptor activity | 0.0338759110886178 |
| GO:0015808 | L-alanine transport | 0.0338759110886178 |
| GO:0015193 | L-proline transmembrane transporter activity | 0.0338759110886178 |
| GO:0016972 | thiol oxidase activity | 0.0338759110886178 |
| GO:0015180 | L-alanine transmembrane transporter activity | 0.0338759110886178 |
| GO:0006880 | intracellular sequestering of iron ion | 0.0338759110886178 |
| GO:0015816 | glycine transport | 0.0338759110886178 |
| GO:0043508 | negative regulation of JNK activity | 0.0338759110886178 |
| GO:0022858 | alanine transmembrane transporter activity | 0.0338759110886178 |
| GO:0016020 | membrane | 0.0338759110886178 |
| GO:0015824 | proline transport | 0.046281544289703 |
| GO:0003071 | renal regulation of systemic arterial blood pressure | 0.046281544289703 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.0479725523165227 |
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>
| Ontology term | p-value | n |
|---|---|---|
| intestine | 6.33e-54 | 17 |
| gastrointestinal system | 3.24e-37 | 25 |
| large intestine | 4.21e-35 | 11 |
| small intestine | 3.34e-28 | 4 |
| colon | 8.11e-28 | 9 |
| vermiform appendix | 1.65e-16 | 1 |
| caecum | 1.65e-16 | 1 |
| midgut | 1.65e-16 | 1 |
| lower digestive tract | 3.23e-13 | 5 |
| digestive system | 1.00e-07 | 145 |
| digestive tract | 1.00e-07 | 145 |
| primitive gut | 1.00e-07 | 145 |
| subdivision of digestive tract | 1.20e-07 | 118 |
| endoderm-derived structure | 6.42e-07 | 160 |
| endoderm | 6.42e-07 | 160 |
| presumptive endoderm | 6.42e-07 | 160 |
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 |
|---|---|---|---|---|
| FOXA1#3169 | 20 | 2.51850448849669 | 9.2020631476479e-05 | 0.00134038252869902 |
| FOXA2#3170 | 16 | 4.47826613684823 | 4.79909341517431e-07 | 2.26281046134262e-05 |
| HNF4A#3172 | 11 | 2.89153629536921 | 0.00145466616250973 | 0.00932506011210125 |
| HNF4G#3174 | 10 | 3.26743437800532 | 0.000979147246418692 | 0.00703599554621726 |
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
