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Coexpression cluster:C4187

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Full id: C4187_colon_gastrointestinal_small_hepatoblastoma_rectum_stomach_duodenum



Phase1 CAGE Peaks

Hg19::chr2:219925637..219925649,-p1@IHH
Hg19::chr2:219925704..219925721,-p3@IHH
Hg19::chr2:219925783..219925786,-p@chr2:219925783..219925786
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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


No results for this coexpression

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


No GOStat results

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>


Cell Type
Ontology termp-valuen
metabolising cell1.85e-0712
endopolyploid cell1.85e-0712
parenchymal cell1.85e-0712
polyploid cell1.85e-0712
hepatocyte1.85e-0712
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract6.54e-11129
endodermal part of digestive tract6.54e-11129
gastrointestinal system2.36e-1035
intestine1.50e-0927
digestive tract diverticulum4.54e-0923
digestive system5.24e-09155
digestive tract5.24e-09155
primitive gut5.24e-09155
endoderm-derived structure2.22e-08169
endoderm2.22e-08169
presumptive endoderm2.22e-08169
epithelium of foregut-midgut junction4.48e-0825
anatomical boundary4.48e-0825
hepatobiliary system4.48e-0825
foregut-midgut junction4.48e-0825
septum transversum4.48e-0825
hepatic diverticulum5.90e-0822
liver primordium5.90e-0822
large intestine9.23e-0811
sac1.21e-0726
gut epithelium2.14e-0754
abdominal segment of trunk4.13e-0761
abdomen4.13e-0761
immaterial anatomical entity5.01e-07126
mixed endoderm/mesoderm-derived structure5.54e-07130
liver9.61e-0719
digestive gland9.61e-0719
liver bud9.61e-0719
Disease
Ontology termp-valuen
gastrointestinal system cancer7.82e-0714


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


This analysis result is provided for C0 - C305 clusters.