Coexpression cluster:C305

Full id: C305_heart_skeletal_smooth_left_bladder_penis_esophagus

Phase1 CAGE Peaks

Hg19::chr19:4518464..4518482,-	p@chr19:4518464..4518482 -
Hg19::chr22:31489256..31489265,+	p16@SMTN
Hg19::chr2:220283091..220283108,+	p1@DES
Hg19::chr2:220284823..220284842,+	p4@DES
Hg19::chr2:220284844..220284884,-	p@chr2:220284844..220284884 -
Hg19::chr2:220284966..220284986,+	p5@DES
Hg19::chr2:220284988..220285027,+	p6@DES
Hg19::chr2:220285210..220285239,+	p@chr2:220285210..220285239 +
Hg19::chr2:220285256..220285296,+	p@chr2:220285256..220285296 +
Hg19::chr2:220285302..220285343,+	p@chr2:220285302..220285343 +
Hg19::chr2:220285541..220285559,+	p@chr2:220285541..220285559 +
Hg19::chr2:220285575..220285610,-	p@chr2:220285575..220285610 -
Hg19::chr2:220285599..220285647,+	p@chr2:220285599..220285647 +
Hg19::chr2:220285612..220285644,-	p@chr2:220285612..220285644 -
Hg19::chr2:220285651..220285664,-	p@chr2:220285651..220285664 -
Hg19::chr2:220286055..220286065,+	p@chr2:220286055..220286065 +
Hg19::chr2:220286085..220286098,+	p@chr2:220286085..220286098 +
Hg19::chr2:220286112..220286136,+	p@chr2:220286112..220286136 +
Hg19::chr2:220286147..220286161,+	p@chr2:220286147..220286161 +
Hg19::chr2:220286168..220286188,+	p@chr2:220286168..220286188 +
Hg19::chr2:220286193..220286205,+	p@chr2:220286193..220286205 +
Hg19::chr2:220290377..220290387,+	p13@DES
Hg19::chr2:220290396..220290425,+	p3@DES
Hg19::chr2:220290408..220290419,-	p@chr2:220290408..220290419 -
Hg19::chr2:220290421..220290473,-	p@chr2:220290421..220290473 -
Hg19::chr2:220290664..220290727,+	p@chr2:220290664..220290727 +
Hg19::chr2:220290729..220290776,+	p@chr2:220290729..220290776 +
Hg19::chr2:220290781..220290803,+	p@chr2:220290781..220290803 +
Hg19::chr2:220290804..220290823,+	p@chr2:220290804..220290823 +
Hg19::chr2:220290830..220290837,+	p@chr2:220290830..220290837 +
Hg19::chr2:220290845..220290851,+	p@chr2:220290845..220290851 +
Hg19::chr2:220290992..220291014,+	p@chr2:220290992..220291014 +
Hg19::chr2:220291020..220291028,+	p@chr2:220291020..220291028 +
Hg19::chr2:220291067..220291084,+	p@chr2:220291067..220291084 +
Hg19::chr2:220291089..220291100,+	p@chr2:220291089..220291100 +
Hg19::chr2:220291155..220291166,+	p@chr2:220291155..220291166 +
Hg19::chr2:220291179..220291201,+	p@chr2:220291179..220291201 +
Hg19::chr2:220291235..220291266,+	p@chr2:220291235..220291266 +
Hg19::chr2:220291318..220291369,-	p1@ENST00000431827
Hg19::chr2:220291449..220291458,-	p@chr2:220291449..220291458 -

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:0003012	muscle system process	0.000644808923970424
GO:0006936	muscle contraction	0.000644808923970424
GO:0045098	type III intermediate filament	0.00215860867718525
GO:0030018	Z disc	0.00917206142502409
GO:0042383	sarcolemma	0.00917206142502409
GO:0031674	I band	0.00917206142502409
GO:0005626	insoluble fraction	0.00924872907672752
GO:0005856	cytoskeleton	0.0103543064344058
GO:0003008	system process	0.0103543064344058
GO:0006939	smooth muscle contraction	0.0103543064344058
GO:0008016	regulation of heart contraction	0.0103543064344058
GO:0008307	structural constituent of muscle	0.0103543064344058
GO:0003015	heart process	0.0103543064344058
GO:0060047	heart contraction	0.0103543064344058
GO:0030017	sarcomere	0.0103543064344058
GO:0030016	myofibril	0.0107175356890367
GO:0044449	contractile fiber part	0.0114181724757752
GO:0043292	contractile fiber	0.0115020737324959
GO:0005200	structural constituent of cytoskeleton	0.014467704270575
GO:0043232	intracellular non-membrane-bound organelle	0.0193433145647536
GO:0043228	non-membrane-bound organelle	0.0193433145647536
GO:0008015	blood circulation	0.0224722302354123
GO:0003013	circulatory system process	0.0224722302354123
GO:0007517	muscle development	0.0231469802933627
GO:0032501	multicellular organismal process	0.0278394694516853
GO:0045111	intermediate filament cytoskeleton	0.0282042822928545
GO:0005882	intermediate filament	0.0282042822928545
GO:0051239	regulation of multicellular organismal process	0.0319025563823224
GO:0015629	actin cytoskeleton	0.0329060306007821
GO:0003779	actin binding	0.046970160060924

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
cell of skeletal muscle	5.82e-13	9

Uber Anatomy

Ontology term	p-value	n
adult organism	2.18e-27	114
cardiac chamber	1.03e-09	3
male genital duct	1.59e-09	3
internal male genitalia	1.59e-09	3
valve	2.49e-09	3
cardiac mesenchyme	2.49e-09	3
cardial valve	2.49e-09	3
tunica intima	2.49e-09	3
heart layer	2.49e-09	3
endocardium	2.49e-09	3
endocardial cushion	2.49e-09	3
presumptive endocardium	2.49e-09	3
intestine	9.83e-09	17
primary circulatory organ	2.55e-07	27
duct of male reproductive system	3.18e-07	4
muscle structure	3.20e-07	2
muscle organ	3.20e-07	2
multi-tissue structure	3.54e-07	342
gastrointestinal system	4.00e-07	25
compound organ	4.13e-07	68
muscle tissue	5.52e-07	64
musculature	5.52e-07	64
musculature of body	5.52e-07	64
cardiac atrium	7.44e-07	2
future cardiac atrium	7.44e-07	2

Disease

Ontology term	p-value	n
heart disease	2.24e-07	2

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
TAL1#6886	5	3.73357708468003	0.0104263657868	0.0386923645811608

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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