Coexpression cluster:C559

Full id: C559_Skeletal_Pericytes_mesenchymal_Myoblast_rhabdomyosarcoma_skeletal_tongue

Phase1 CAGE Peaks

Hg19::chr11:17716498..17716504,+	p2@ENST00000524885
Hg19::chr11:17741111..17741124,+	p1@MYOD1
Hg19::chr11:17741254..17741282,+	p2@MYOD1
Hg19::chr11:64012815..64012824,-	p20@PPP1R14B
Hg19::chr11:85090324..85090329,-	p@chr11:85090324..85090329 -
Hg19::chr13:99582467..99582528,-	p@chr13:99582467..99582528 -
Hg19::chr17:38502981..38502987,+	p@chr17:38502981..38502987 +
Hg19::chr22:20103621..20103632,+	p14@RANBP1
Hg19::chr22:20103644..20103662,+	p10@RANBP1
Hg19::chr6:169588511..169588525,-	p@chr6:169588511..169588525 -
Hg19::chr6:169588532..169588548,-	p@chr6:169588532..169588548 -
Hg19::chr6:169588553..169588570,-	p@chr6:169588553..169588570 -
Hg19::chr6:169588594..169588599,-	p@chr6:169588594..169588599 -
Hg19::chr6:2783611..2783617,+	p5@U56249
Hg19::chr6:2783684..2783703,+	p1@U56249
Hg19::chr6:2783707..2783715,+	p2@U56249

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:0048625	myoblast cell fate commitment	0.0229580571962169
GO:0007518	myoblast cell fate determination	0.0229580571962169
GO:0000731	DNA synthesis during DNA repair	0.0306039852584672
GO:0030174	regulation of DNA replication initiation	0.0306039852584672
GO:0008536	Ran GTPase binding	0.0336599244224942
GO:0045445	myoblast differentiation	0.0427812955751279
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0427812955751279
GO:0005092	GDP-dissociation inhibitor activity	0.0427812955751279
GO:0006275	regulation of DNA replication	0.0427812955751279
GO:0001709	cell fate determination	0.0427812955751279
GO:0004864	protein phosphatase inhibitor activity	0.0427812955751279
GO:0019212	phosphatase inhibitor activity	0.0427812955751279
GO:0006270	DNA replication initiation	0.0427812955751279
GO:0048741	skeletal muscle fiber development	0.0427812955751279
GO:0048747	muscle fiber development	0.0427812955751279
GO:0042692	muscle cell differentiation	0.0439194635543592
GO:0051052	regulation of DNA metabolic process	0.0440259557804808

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	1.88e-82	9
skeletal muscle satellite cell	3.28e-21	3
muscle precursor cell	1.69e-20	58
myoblast	1.69e-20	58
multi-potent skeletal muscle stem cell	1.69e-20	58
contractile cell	4.76e-16	59
skeletal muscle myoblast	6.61e-16	4
muscle cell	3.05e-13	55
electrically responsive cell	6.77e-12	61
electrically active cell	6.77e-12	61
non-terminally differentiated cell	1.19e-10	106
mesodermal cell	2.05e-09	121
central nervous system pericyte	4.02e-09	2

Uber Anatomy

Ontology term	p-value	n
skeletal muscle tissue	3.95e-19	62
striated muscle tissue	3.95e-19	62
myotome	3.95e-19	62
muscle tissue	1.65e-18	64
musculature	1.65e-18	64
musculature of body	1.65e-18	64
somite	1.30e-16	71
presomitic mesoderm	1.30e-16	71
presumptive segmental plate	1.30e-16	71
dermomyotome	1.30e-16	71
trunk paraxial mesoderm	1.30e-16	71
paraxial mesoderm	2.26e-16	72
presumptive paraxial mesoderm	2.26e-16	72
dense mesenchyme tissue	3.88e-16	73
epithelial vesicle	4.70e-15	78
multilaminar epithelium	4.22e-14	83
trunk mesenchyme	2.49e-09	122
throat	6.42e-09	2
unilaminar epithelium	1.56e-07	148
mesenchyme	6.70e-07	160
entire embryonic mesenchyme	6.70e-07	160

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.