Coexpression cluster:C4270

Full id: C4270_mucinous_pleomorphic_signet_thyroid_bile_oral_tubular

Phase1 CAGE Peaks

Hg19::chr3:115509849..115509867,+	p@chr3:115509849..115509867 +
Hg19::chr3:115509871..115509888,+	p@chr3:115509871..115509888 +
Hg19::chr3:115648872..115648875,+	p@chr3:115648872..115648875 +

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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No GOStat results

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
glial cell (sensu Vertebrata)	5.33e-09	15
glial cell	5.33e-09	15
glioblast	5.33e-09	15
glioblast (sensu Vertebrata)	5.33e-09	15
neuron associated cell	8.13e-08	17
neuron associated cell (sensu Vertebrata)	8.13e-08	17

Uber Anatomy

Ontology term	p-value	n
mucosa of oral region	8.95e-08	4
respiratory system mucosa	8.95e-08	4
atypical epithelium	2.21e-07	4

Disease

Ontology term	p-value	n
carcinoma	2.76e-17	106
cell type cancer	5.05e-13	143
disease of cellular proliferation	3.31e-10	239
disease of anatomical entity	1.36e-09	39
cancer	1.50e-09	235
squamous cell carcinoma	1.22e-08	14

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
FOSL1#8061	2	26.4757198109153	0.00186983370259098	0.0110267398116826
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376847739892529
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225990848403897
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164510453041843
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460597413720311
PRDM1#639	2	87.8873038516405	0.000171624884802908	0.00209200879364273
SMARCA4#6597	2	104.510602205259	0.000121451859247127	0.00164496313421226
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0330009673291792
SMARCC1#6599	2	29.1089062130876	0.00154920081422414	0.00984406083212185
SMARCC2#6601	2	62.7702496179317	0.000335837541708507	0.00341790460129553
SMC3#9126	2	10.0299552299552	0.012665637976747	0.04577274523871
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287575980763803
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329294861736342
ZNF274#10782	2	947.83076923077	1.47205921117966e-06	5.68566538300267e-05

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.