Coexpression cluster:C1021

Full id: C1021_Small_Bronchial_Tracheal_Mallassezderived_Gingival_Sebocyte_squamous

Phase1 CAGE Peaks

Hg19::chr12:56332022..56332030,+	p17@DGKA
Hg19::chr1:153537328..153537329,-	p5@S100A2
Hg19::chr1:183133608..183133625,-	p@chr1:183133608..183133625 -
Hg19::chr1:209827500..209827512,-	p@chr1:209827500..209827512 -
Hg19::chr1:209827520..209827532,-	p@chr1:209827520..209827532 -
Hg19::chr8:29526932..29526947,-	p@chr8:29526932..29526947 -
Hg19::chr8:49783129..49783154,+	p@chr8:49783129..49783154 +
Hg19::chr9:21683189..21683195,+	p@chr9:21683189..21683195 +

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:0043542	endothelial cell migration	0.0262720383888429
GO:0004143	diacylglycerol kinase activity	0.0262720383888429
GO:0005509	calcium ion binding	0.0262720383888429
GO:0007205	protein kinase C activation	0.0262720383888429
GO:0019992	diacylglycerol binding	0.0322487025371141
GO:0032147	activation of protein kinase activity	0.0322487025371141
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0347404066847027
GO:0048015	phosphoinositide-mediated signaling	0.0368975161749926
GO:0045860	positive regulation of protein kinase activity	0.0368975161749926
GO:0033674	positive regulation of kinase activity	0.0368975161749926
GO:0051347	positive regulation of transferase activity	0.0368975161749926
GO:0016477	cell migration	0.0434492764139489
GO:0045859	regulation of protein kinase activity	0.0434492764139489
GO:0043549	regulation of kinase activity	0.0434492764139489
GO:0051338	regulation of transferase activity	0.0434492764139489
GO:0043085	positive regulation of catalytic activity	0.0434492764139489
GO:0019932	second-messenger-mediated signaling	0.0434492764139489

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	3.01e-21	254
endo-epithelial cell	1.01e-15	43
squamous epithelial cell	6.16e-15	62
endodermal cell	4.63e-11	59
animal cell	5.37e-11	679
eukaryotic cell	5.37e-11	679
embryonic cell	3.61e-10	248
respiratory epithelial cell	1.56e-09	13

Uber Anatomy

Ontology term	p-value	n
anatomical group	1.32e-09	626
anatomical system	1.76e-09	625
female organism	3.64e-09	41
mesoderm	5.79e-08	448
mesoderm-derived structure	5.79e-08	448
presumptive mesoderm	5.79e-08	448
multi-cellular organism	8.55e-08	659
female reproductive organ	1.61e-07	37
female reproductive system	1.61e-07	37
germ layer	5.85e-07	604
embryonic tissue	5.85e-07	604
presumptive structure	5.85e-07	604
epiblast (generic)	5.85e-07	604
embryonic structure	7.67e-07	605
developing anatomical structure	7.67e-07	605

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.04e-09	14
female reproductive organ cancer	4.55e-07	27

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
CEBPB#1051	5	4.98196726614051	0.00125052377879302	0.00840542237954462
STAT3#6774	5	6.5746656232214	0.000339446577241864	0.00345059967690899
TCF7L2#6934	4	5.38508828156867	0.00382581463501135	0.0188785379005882

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.