Coexpression cluster:C341

Full id: C341_giant_large_Fibroblast_Mesenchymal_Alveolar_Mesothelial_mesothelioma

Phase1 CAGE Peaks

Hg19::chr10:4828673..4828695,+	p10@AKR1E2
Hg19::chr10:4828763..4828786,+	p7@AKR1E2
Hg19::chr10:4828815..4828822,+	p11@AKR1E2
Hg19::chr10:4828859..4828883,+	p6@AKR1E2
Hg19::chr10:4832416..4832424,-	p@chr10:4832416..4832424 -
Hg19::chr11:28723970..28723983,+	p3@ENST00000513853
Hg19::chr11:28724030..28724037,+	p6@ENST00000513853
Hg19::chr12:120662266..120662274,-	p65@PXN
Hg19::chr12:120662499..120662559,-	p3@PXN
Hg19::chr12:120662701..120662711,-	p58@PXN
Hg19::chr12:120662730..120662751,-	p46@PXN
Hg19::chr12:26126668..26126674,+	p27@RASSF8
Hg19::chr12:26126681..26126692,+	p8@RASSF8
Hg19::chr12:66035928..66035945,-	p1@ENST00000535315 p1@ENST00000537298
Hg19::chr12:66035968..66035976,-	p1@ENST00000537250
Hg19::chr12:66035982..66035985,-	p3@ENST00000537250
Hg19::chr12:66035988..66035995,-	p2@ENST00000537250
Hg19::chr12:66036060..66036071,-	p4@ENST00000539653
Hg19::chr12:66036083..66036098,-	p3@ENST00000539653
Hg19::chr12:66036125..66036136,-	p2@ENST00000539653
Hg19::chr12:66036137..66036157,-	p1@ENST00000539653 p2@ENST00000544557
Hg19::chr12:66036191..66036200,-	p3@ENST00000544557
Hg19::chr12:66036219..66036262,-	p1@ENST00000544557
Hg19::chr15:33384526..33384543,-	p@chr15:33384526..33384543 -
Hg19::chr15:33384561..33384569,-	p@chr15:33384561..33384569 -
Hg19::chr1:172902742..172902768,-	p@chr1:172902742..172902768 -
Hg19::chr2:239344630..239344631,+	p20@ASB1
Hg19::chr2:36805997..36806020,-	p10@FEZ2
Hg19::chr2:36806173..36806191,-	p14@FEZ2
Hg19::chr2:36806197..36806224,-	p11@FEZ2
Hg19::chr2:36806228..36806237,-	p24@FEZ2
Hg19::chr2:36806248..36806258,-	p23@FEZ2
Hg19::chr5:14200357..14200390,+	p@chr5:14200357..14200390 +

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:0007165	signal transduction	0.0175341130992519
GO:0017166	vinculin binding	0.0175341130992519
GO:0007154	cell communication	0.0175341130992519
GO:0051674	localization of cell	0.0175341130992519
GO:0006928	cell motility	0.0175341130992519
GO:0030539	male genitalia development	0.0206567778714676
GO:0048806	genitalia development	0.0236046189169336
GO:0042036	negative regulation of cytokine biosynthetic process	0.0244745405962095
GO:0007172	signal complex assembly	0.0244745405962095
GO:0046546	development of primary male sexual characteristics	0.0357782122939305
GO:0046661	male sex differentiation	0.0400209603080005
GO:0017148	negative regulation of translation	0.0469851050101578
GO:0031327	negative regulation of cellular biosynthetic process	0.047384859189351
GO:0009890	negative regulation of biosynthetic process	0.047384859189351
GO:0007411	axon guidance	0.047384859189351
GO:0045137	development of primary sexual characteristics	0.047384859189351
GO:0042035	regulation of cytokine biosynthetic process	0.047384859189351
GO:0042089	cytokine biosynthetic process	0.047384859189351
GO:0042107	cytokine metabolic process	0.047384859189351
GO:0043623	cellular protein complex assembly	0.047384859189351

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
lung large cell carcinoma	5.96e-34	3
non-small cell lung carcinoma	5.15e-21	5
lung carcinoma	2.45e-12	9
lung cancer	5.93e-08	15
respiratory system cancer	1.54e-07	16

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
EP300#2033	12	2.46325153680844	0.00181435430642365	0.0108983349288882
RAD21#5885	12	3.76546687107503	3.32121315067201e-05	0.000660065043278848
STAT3#6774	8	2.55017333264345	0.0105509167498914	0.0389897103687606
TCF7L2#6934	12	3.91642784114085	2.23995125295158e-05	0.000490025699428174

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.