Coexpression cluster:C1244

Full id: C1244_Smooth_mesenchymal_Fibroblast_mesothelioma_gall_Melanocyte_meningioma

Phase1 CAGE Peaks

Hg19::chr19:56070737..56070738,-	p@chr19:56070737..56070738 -
Hg19::chr1:27992577..27992588,+	p@chr1:27992577..27992588 +
Hg19::chr1:27992792..27992807,-	p@chr1:27992792..27992807 -
Hg19::chr1:27992888..27992908,+	p@chr1:27992888..27992908 +
Hg19::chr1:27998692..27998710,-	p1@IFI6
Hg19::chr21:42798552..42798557,+	p17@MX1
Hg19::chr22:18632879..18632890,+	p4@USP18

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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p.value	FDR	nGenes	nPathway	Name
5.70320151504265e-06	0.00361012655902199	3	511	Signaling in Immune system (Reactome):REACT_6900
2.94296390254009e-05	0.00931448075153939	2	90	IL-4 down reg. targets (Netpath):NetPath_16

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:0051902	negative regulation of mitochondrial depolarization	0.0142023708595349
GO:0051900	regulation of mitochondrial depolarization	0.0142023708595349
GO:0051882	mitochondrial depolarization	0.0142023708595349
GO:0043154	negative regulation of caspase activity	0.0142023708595349
GO:0051899	membrane depolarization	0.0142023708595349
GO:0042981	regulation of apoptosis	0.0142023708595349
GO:0043067	regulation of programmed cell death	0.0142023708595349
GO:0051881	regulation of mitochondrial membrane potential	0.0142023708595349
GO:0001836	release of cytochrome c from mitochondria	0.014918783863124
GO:0008637	apoptotic mitochondrial changes	0.0175732208981636
GO:0006915	apoptosis	0.0175732208981636
GO:0012501	programmed cell death	0.0175732208981636
GO:0016265	death	0.0175732208981636
GO:0008219	cell death	0.0175732208981636
GO:0042391	regulation of membrane potential	0.0213340273481574
GO:0048468	cell development	0.0285858889496168
GO:0043281	regulation of caspase activity	0.0364027197571902
GO:0008632	apoptotic program	0.0457389008459905
GO:0007005	mitochondrion organization and biogenesis	0.0457389008459905
GO:0048869	cellular developmental process	0.0457389008459905
GO:0030154	cell differentiation	0.0457389008459905
GO:0009615	response to virus	0.0458932399910274

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><br>

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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
STAT2#6773	2	18.6467917675545	0.00468275705257902	0.0220945319093879

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.