Coexpression cluster:C3544

Full id: C3544_colon_signet_gastric_gall_stomach_adenocarcinoma_bile

Phase1 CAGE Peaks

Hg19::chr16:23724518..23724568,-	p1@ERN2
Hg19::chr19:18366144..18366181,-	p1@PDE4C
Hg19::chr19:18366182..18366210,-	p3@PDE4C

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0016075	rRNA catabolic process	0.0144823018523883
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0253421630918994
GO:0016788	hydrolase activity, acting on ester bonds	0.0469431554649212
GO:0016891	endoribonuclease activity, producing 5'-phosphomonoesters	0.0485869538368147
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0485869538368147
GO:0006401	RNA catabolic process	0.0485869538368147
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0485869538368147
GO:0016893	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0497440775346638

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	7.81e-20	160
endoderm	7.81e-20	160
presumptive endoderm	7.81e-20	160
digestive system	2.18e-15	145
digestive tract	2.18e-15	145
primitive gut	2.18e-15	145
subdivision of digestive tract	3.26e-15	118
gastrointestinal system	9.82e-12	25
intestine	5.30e-10	17
biliary system	6.38e-09	9
biliary tree	6.38e-09	9
biliary bud	6.38e-09	9
gallbladder	2.90e-08	3
gall bladder primordium	2.90e-08	3
small intestine	4.11e-08	4
renal system	6.82e-07	48

Disease

Ontology term	p-value	n
adenocarcinoma	7.12e-08	25

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378078714707467

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

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This analysis result is provided for C0 - C305 clusters.