Coexpression cluster:C365

Full id: C365_trachea_throat_aorta_lung_parotid_salivary_umbilical

Phase1 CAGE Peaks

Hg19::chr10:13276329..13276338,-	p3@UCMA
Hg19::chr10:13276352..13276361,-	p2@UCMA
Hg19::chr10:13276368..13276379,-	p1@UCMA
Hg19::chr11:34909983..34910006,-	p@chr11:34909983..34910006 -
Hg19::chr12:10998450..10998451,+	p@chr12:10998450..10998451 +
Hg19::chr12:119772810..119772834,+	p4@CCDC60
Hg19::chr12:48390329..48390340,+	p@chr12:48390329..48390340 +
Hg19::chr16:78056435..78056451,+	p1@CLEC3A
Hg19::chr17:10276319..10276324,-	p1@MYH13
Hg19::chr19:41620335..41620338,+	p1@CYP2F1
Hg19::chr1:31196427..31196433,-	p1@MATN1
Hg19::chr22:37215541..37215544,-	p3@PVALB
Hg19::chr2:180524914..180524925,-	p17@ZNF385B
Hg19::chr5:147261651..147261660,+	p@chr5:147261651..147261660 +
Hg19::chr5:147526410..147526417,+	p@chr5:147526410..147526417 +
Hg19::chr5:180017106..180017107,+	p@chr5:180017106..180017107 +
Hg19::chr5:180017127..180017161,-	p@chr5:180017127..180017161 -
Hg19::chr5:180017171..180017202,+	p@chr5:180017171..180017202 +
Hg19::chr5:180017205..180017215,-	p@chr5:180017205..180017215 -
Hg19::chr5:180017253..180017257,-	p@chr5:180017253..180017257 -
Hg19::chr5:180017672..180017683,-	p11@SCGB3A1
Hg19::chr5:180017691..180017700,-	p8@SCGB3A1
Hg19::chr5:180017732..180017767,-	p3@SCGB3A1
Hg19::chr5:180017818..180017830,-	p7@SCGB3A1
Hg19::chr5:180018490..180018505,-	p1@SCGB3A1
Hg19::chr5:180018695..180018706,-	p9@SCGB3A1
Hg19::chr6:70937124..70937126,-	p@chr6:70937124..70937126 -
Hg19::chr6:71012780..71012794,-	p2@COL9A1
Hg19::chr7:75368627..75368651,+	p@chr7:75368627..75368651 +
Hg19::chr9:38720126..38720131,-	p@chr9:38720126..38720131 -

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:0005201	extracellular matrix structural constituent	0.000213322837143487
GO:0044421	extracellular region part	0.00111610238361664
GO:0005578	proteinaceous extracellular matrix	0.00282570299014515
GO:0048856	anatomical structure development	0.0121855798442595
GO:0005594	collagen type IX	0.0164400489879395
GO:0001501	skeletal development	0.017181818860989
GO:0048513	organ development	0.0205446175102198
GO:0005593	FACIT collagen	0.0205446175102198
GO:0030934	anchoring collagen	0.0273855671839068
GO:0001502	cartilage condensation	0.0291932207385848
GO:0032502	developmental process	0.0291932207385848
GO:0000146	microfilament motor activity	0.0291932207385848
GO:0048731	system development	0.0291932207385848
GO:0032982	myosin filament	0.0291932207385848
GO:0005863	striated muscle thick filament	0.0291932207385848
GO:0032501	multicellular organismal process	0.0351270622408377
GO:0005859	muscle myosin complex	0.0374187747719306
GO:0016460	myosin II complex	0.0374187747719306
GO:0050381	unspecific monooxygenase activity	0.0374187747719306
GO:0030424	axon	0.0459438181410297
GO:0051216	cartilage development	0.0459438181410297
GO:0006941	striated muscle contraction	0.0459438181410297

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>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
open tracheal system trachea	3.99e-41	2
throat	8.98e-41	2
surface	4.22e-21	1
trachea	1.59e-12	7
respiratory airway	1.59e-12	7
thoracic cavity element	9.38e-10	34
thoracic cavity	9.38e-10	34
thoracic segment organ	1.74e-09	35
neck	5.57e-09	10
respiratory primordium	9.23e-09	38
endoderm of foregut	9.23e-09	38

Disease

Ontology term	p-value	n
vascular disease	7.72e-21	1
ischemia	7.72e-21	1
extrinsic cardiomyopathy	7.72e-21	1
myocardial ischemia	7.72e-21	1
myocardial infarction	7.72e-21	1
heart disease	4.09e-11	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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No analysis results for this cluster

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.