Coexpression cluster:C3976

Full id: C3976_testicular_extraskeletal_cervical_maxillary_teratocarcinoma_iPS_H9

Phase1 CAGE Peaks

Hg19::chr1:36020462..36020478,-	p21@KIAA0319L
Hg19::chr3:99980143..99980163,+	p4@TBC1D23
Hg19::chr3:99980167..99980181,+	p5@TBC1D23

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:0005097	Rab GTPase activator activity	0.0239567038401373
GO:0032313	regulation of Rab GTPase activity	0.0239567038401373
GO:0032482	Rab protein signal transduction	0.0239567038401373
GO:0032483	regulation of Rab protein signal transduction	0.0239567038401373
GO:0005099	Ras GTPase activator activity	0.0239567038401373
GO:0032318	regulation of Ras GTPase activity	0.0239567038401373
GO:0043087	regulation of GTPase activity	0.0239567038401373
GO:0051336	regulation of hydrolase activity	0.0269087147398698
GO:0005096	GTPase activator activity	0.0269087147398698
GO:0046578	regulation of Ras protein signal transduction	0.0269087147398698
GO:0007265	Ras protein signal transduction	0.0269087147398698
GO:0008047	enzyme activator activity	0.0269087147398698
GO:0005083	small GTPase regulator activity	0.0269087147398698
GO:0051056	regulation of small GTPase mediated signal transduction	0.0269087147398698
GO:0050790	regulation of catalytic activity	0.0320558106676086
GO:0065009	regulation of a molecular function	0.0327259126893428
GO:0030695	GTPase regulator activity	0.0327259126893428
GO:0009966	regulation of signal transduction	0.0353232073472271
GO:0007264	small GTPase mediated signal transduction	0.0365595196043801

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><br>disease_data<br>

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Disease

Ontology term	p-value	n
carcinoma	7.14e-09	106
squamous cell carcinoma	6.37e-08	14
disease of cellular proliferation	3.92e-07	239

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)
{{{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

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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
ATF3#467	2	14.9754496840058	0.00576829454079388	0.0259591896214923
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225929874166537
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246761522011571
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179727307806115
POU5F1#5460	1	111.813067150635	0.00891691105511183	0.0338238940066402
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329937566298356

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.