Coexpression cluster:C3302

Full id: C3302_Skeletal_diaphragm_skeletal_penis_throat_tongue_epididymis

Phase1 CAGE Peaks

Hg19::chr12:56547669..56547684,+	p2@MYL6B
Hg19::chr1:201399016..201399025,-	p4@TNNI1
Hg19::chr2:219696548..219696558,-	p2@PRKAG3

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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p.value	FDR	nGenes	nPathway	Name
8.64980401661253e-06	0.00547532594251573	2	49	Muscle contraction (Reactome):REACT_17044

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:0044449	contractile fiber part	0.000486784263842463
GO:0043292	contractile fiber	0.000486784263842463
GO:0003012	muscle system process	0.00163023820085446
GO:0006936	muscle contraction	0.00163023820085446
GO:0004679	AMP-activated protein kinase activity	0.00164252914164606
GO:0015629	actin cytoskeleton	0.00349803528037607
GO:0030049	muscle filament sliding	0.00513229919892161
GO:0033275	actin-myosin filament sliding	0.00513229919892161
GO:0005861	troponin complex	0.00547429132176457
GO:0016461	unconventional myosin complex	0.00574783667623449
GO:0006942	regulation of striated muscle contraction	0.00597160256409073
GO:0005865	striated muscle thin filament	0.00752604267770224
GO:0030048	actin filament-based movement	0.0101034090920804
GO:0005523	tropomyosin binding	0.0123117172763509
GO:0044430	cytoskeletal part	0.0125512755839534
GO:0005859	muscle myosin complex	0.0125512755839534
GO:0016460	myosin II complex	0.0125512755839534
GO:0006941	striated muscle contraction	0.0168386859144542
GO:0006937	regulation of muscle contraction	0.0168386859144542
GO:0008307	structural constituent of muscle	0.0172257490857199
GO:0030017	sarcomere	0.018745801989806
GO:0030016	myofibril	0.019754740012505
GO:0005856	cytoskeleton	0.0205045017426492
GO:0007519	skeletal muscle development	0.0221987265916081
GO:0003008	system process	0.0221987265916081
GO:0006633	fatty acid biosynthetic process	0.0230097446059705
GO:0016053	organic acid biosynthetic process	0.0242859114184931
GO:0046394	carboxylic acid biosynthetic process	0.0242859114184931
GO:0014706	striated muscle development	0.0248573624476498
GO:0016459	myosin complex	0.0292004645054482
GO:0007517	muscle development	0.0453379495687452
GO:0006631	fatty acid metabolic process	0.0484986753684516
GO:0030705	cytoskeleton-dependent intracellular transport	0.0484986753684516

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><br>

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Cell Type

Ontology term	p-value	n
cell of skeletal muscle	5.33e-10	9

Uber Anatomy

Ontology term	p-value	n
adult organism	6.76e-10	115
skeletal muscle tissue	5.08e-08	61
striated muscle tissue	5.08e-08	61
myotome	5.08e-08	61
muscle tissue	1.56e-07	63
musculature	1.56e-07	63
musculature of body	1.56e-07	63
posterior neural tube	2.74e-07	15
chordal neural plate	2.74e-07	15

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)
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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.