Coexpression cluster:C1425

Full id: C1425_umbilical_skeletal_heart_penis_left_vein_diaphragm

Phase1 CAGE Peaks

Hg19::chr16:7382818..7382819,+	p40@RBFOX1
Hg19::chr2:106115231..106115234,+	p@chr2:106115231..106115234 +
Hg19::chr2:179629521..179629528,-	p138@TTN
Hg19::chr2:220495902..220495903,+	p25@SLC4A3
Hg19::chr4:100578977..100578989,-	p@chr4:100578977..100578989 -
Hg19::chr4:23890694..23890699,-	p@chr4:23890694..23890699 -

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:0051393	alpha-actinin binding	0.0119301652014414
GO:0042805	actinin binding	0.0119301652014414
GO:0030239	myofibril assembly	0.0119301652014414
GO:0055001	muscle cell development	0.0119301652014414
GO:0055002	striated muscle cell development	0.0119301652014414
GO:0017022	myosin binding	0.0119301652014414
GO:0048628	myoblast maturation	0.0123024395660017
GO:0048627	myoblast development	0.0123024395660017
GO:0030018	Z disc	0.0138263140820198
GO:0051146	striated muscle cell differentiation	0.0138263140820198
GO:0031674	I band	0.0138263140820198
GO:0031032	actomyosin structure organization and biogenesis	0.0152355730671411
GO:0045445	myoblast differentiation	0.0152355730671411
GO:0015106	bicarbonate transmembrane transporter activity	0.0152355730671411
GO:0000794	condensed nuclear chromosome	0.0152355730671411
GO:0005452	inorganic anion exchanger activity	0.0152355730671411
GO:0015380	anion exchanger activity	0.0152355730671411
GO:0015301	anion:anion antiporter activity	0.0152355730671411
GO:0015108	chloride transmembrane transporter activity	0.0152355730671411
GO:0006941	striated muscle contraction	0.0152355730671411
GO:0048741	skeletal muscle fiber development	0.0152355730671411
GO:0008307	structural constituent of muscle	0.0152355730671411
GO:0048747	muscle fiber development	0.0152355730671411
GO:0046777	protein amino acid autophosphorylation	0.0152355730671411
GO:0048469	cell maturation	0.0152355730671411
GO:0042692	muscle cell differentiation	0.0152355730671411
GO:0016540	protein autoprocessing	0.0152355730671411
GO:0030017	sarcomere	0.0152874174755057
GO:0000793	condensed chromosome	0.0152874174755057
GO:0030016	myofibril	0.0152874174755057
GO:0021700	developmental maturation	0.0152874174755057
GO:0044449	contractile fiber part	0.0167639532257972
GO:0043292	contractile fiber	0.0173386632132831
GO:0007519	skeletal muscle development	0.0176167693313917
GO:0015103	inorganic anion transmembrane transporter activity	0.0181340618399547
GO:0014706	striated muscle development	0.0218462131870707
GO:0015297	antiporter activity	0.0219794318898589
GO:0016485	protein processing	0.0226827744463691
GO:0000228	nuclear chromosome	0.0226827744463691
GO:0005516	calmodulin binding	0.031478625965811
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0327321340518741
GO:0035023	regulation of Rho protein signal transduction	0.0327321340518741
GO:0003012	muscle system process	0.0327321340518741
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0327321340518741
GO:0006936	muscle contraction	0.0327321340518741
GO:0007517	muscle development	0.0333755668419712
GO:0007266	Rho protein signal transduction	0.0356956654106276
GO:0008509	anion transmembrane transporter activity	0.0388441760135324
GO:0007067	mitosis	0.0431821166596885
GO:0000087	M phase of mitotic cell cycle	0.0431821166596885
GO:0030036	actin cytoskeleton organization and biogenesis	0.0431821166596885
GO:0030029	actin filament-based process	0.0445721666664363

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
primary circulatory organ	2.86e-27	27
valve	3.63e-21	3
cardiac mesenchyme	3.63e-21	3
cardial valve	3.63e-21	3
tunica intima	3.63e-21	3
heart layer	3.63e-21	3
endocardium	3.63e-21	3
endocardial cushion	3.63e-21	3
presumptive endocardium	3.63e-21	3
hindlimb bud	5.53e-17	1
soleus muscle	5.53e-17	1
appendage	5.53e-17	1
lower limb segment	5.53e-17	1
multi-limb segment region	5.53e-17	1
hindlimb muscle	5.53e-17	1
hindlimb zeugopod muscle	5.53e-17	1
paired limb/fin	5.53e-17	1
limb	5.53e-17	1
pelvic appendage	5.53e-17	1
limb segment	5.53e-17	1
paired limb/fin segment	5.53e-17	1
limb muscle	5.53e-17	1
pelvic complex muscle	5.53e-17	1
zeugopod	5.53e-17	1
muscle of leg	5.53e-17	1
paired limb/fin bud	5.53e-17	1
limb bud	5.53e-17	1
pelvic appendage bud	5.53e-17	1
limb/fin field	5.53e-17	1
subdivision of organism along appendicular axis	5.53e-17	1
appendage girdle complex	5.53e-17	1
leg	5.53e-17	1
hindlimb	5.53e-17	1
triceps surae	5.53e-17	1
hindlimb zeugopod	5.53e-17	1
posterior region of body	5.53e-17	1
pelvic complex	5.53e-17	1
limb field	5.53e-17	1
hindlimb/pelvic fin field	5.53e-17	1
pulmonary valve	1.41e-16	1
semi-lunar valve	1.41e-16	1
left cardiac atrium	1.65e-16	1
mitral valve	1.93e-16	1
compound organ	9.77e-14	68
adult organism	1.84e-12	114
heart	1.77e-10	24
primitive heart tube	1.77e-10	24
primary heart field	1.77e-10	24
anterior lateral plate mesoderm	1.77e-10	24
heart tube	1.77e-10	24
heart primordium	1.77e-10	24
cardiac mesoderm	1.77e-10	24
cardiogenic plate	1.77e-10	24
heart rudiment	1.77e-10	24
blood vessel layer	1.24e-09	7
muscle structure	3.71e-09	2
muscle organ	3.71e-09	2
cardiac atrium	6.42e-09	2
future cardiac atrium	6.42e-09	2
atrioventricular valve	6.94e-09	2
throat	7.49e-09	2
neural crest-derived structure	5.26e-07	10
neural crest	5.26e-07	10
neural fold	5.26e-07	10

Disease

Ontology term	p-value	n
heart disease	8.57e-32	2
vascular disease	1.04e-16	1
ischemia	1.04e-16	1
extrinsic cardiomyopathy	1.04e-16	1
myocardial ischemia	1.04e-16	1
myocardial infarction	1.04e-16	1
cardiovascular system disease	1.93e-16	4

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.