Coexpression cluster:C2372

Full id: C2372_pancreas_kidney_duodenum_small_temporal_Intestinal_colon

Phase1 CAGE Peaks

Hg19::chr16:3704862..3704880,+	p3@DNASE1
Hg19::chr1:43751517..43751532,-	p3@C1orf210
Hg19::chr4:70032343..70032354,+	p@chr4:70032343..70032354 +
Hg19::chr8:52886175..52886189,+	p@chr8:52886175..52886189 +

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:0004530	deoxyribonuclease I activity	0.00317908866125044
GO:0016888	endodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.0254270943443241
GO:0004520	endodeoxyribonuclease activity	0.0278031053997779
GO:0006308	DNA catabolic process	0.0278031053997779
GO:0004536	deoxyribonuclease activity	0.0291184844105349
GO:0016893	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0291184844105349

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>

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Cell Type

Ontology term	p-value	n
epithelial cell of stomach	4.19e-10	3
serous secreting cell	2.46e-08	1

Uber Anatomy

Ontology term	p-value	n
gastrointestinal system	5.84e-21	25
intestine	3.80e-14	17
small intestine	5.11e-14	4
stomach	2.20e-08	8
food storage organ	2.20e-08	8
epididymis	2.29e-08	1
epithelium of female gonad	2.46e-08	1
subdivision of digestive tract	1.04e-07	118

Disease

Ontology term	p-value	n
signet ring cell adenocarcinoma	1.16e-14	2
ovary epithelial cancer	2.46e-08	1
adenocarcinoma	9.00e-07	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
ESRRA#2101	1	120.960078534031	0.00824166246177904	0.0324836208712258
FOXA2#3170	2	12.3152318763326	0.00936191628546724	0.0353399058422638
HNF4G#3174	2	14.3767112632234	0.00692416998043918	0.0293023780780051

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.