Coexpression cluster:C519

Full id: C519_Preadipocyte_Ewing_Myoblast_spindle_Fibroblast_Adipocyte_Osteoblast

Phase1 CAGE Peaks

Hg19::chr6:35181725..35181742,+	p3@SCUBE3
Hg19::chr6:35181783..35181815,+	p2@SCUBE3
Hg19::chr6:35181816..35181850,+	p1@SCUBE3
Hg19::chr6:35181866..35181878,+	p7@SCUBE3
Hg19::chr6:35181935..35181948,+	p4@SCUBE3
Hg19::chr6:35181964..35181980,+	p5@SCUBE3
Hg19::chr6:35182176..35182190,+	p6@SCUBE3
Hg19::chr6:35200689..35200695,+	p9@SCUBE3
Hg19::chr6:35211380..35211391,+	p@chr6:35211380..35211391 +
Hg19::chr6:35214004..35214032,+	p@chr6:35214004..35214032 +
Hg19::chr6:35216360..35216374,+	p10@SCUBE3
Hg19::chr6:35217101..35217114,+	p@chr6:35217101..35217114 +
Hg19::chr6:35218080..35218089,+	p@chr6:35218080..35218089 +
Hg19::chr6:35218158..35218175,+	p@chr6:35218158..35218175 +
Hg19::chr6:35218350..35218364,+	p2@AK123742
Hg19::chr6:35218435..35218446,+	p4@AK123742
Hg19::chr6:35218509..35218513,+	p1@AK123742
Hg19::chr6:35219318..35219336,+	p3@AK123742

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:0048196	middle lamella-containing extracellular matrix	0.000183975038266808
GO:0009505	cellulose and pectin-containing cell wall	0.000183975038266808
GO:0048222	glycoprotein network	0.000183975038266808
GO:0009530	primary cell wall	0.000183975038266808
GO:0005618	cell wall	0.000294360061226893
GO:0044462	external encapsulating structure part	0.000490600102044821
GO:0030312	external encapsulating structure	0.000630771559771913
GO:0051291	protein heterooligomerization	0.000735900153067232
GO:0051260	protein homooligomerization	0.00335243403063961
GO:0051259	protein oligomerization	0.00456258094901684
GO:0044420	extracellular matrix part	0.00876390182289157
GO:0009986	cell surface	0.00907610188782919
GO:0006461	protein complex assembly	0.0192466193879122
GO:0065003	macromolecular complex assembly	0.0397386082656305
GO:0022607	cellular component assembly	0.0398857882962439

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
non-terminally differentiated cell	3.03e-33	180
fibroblast	7.32e-14	75
muscle precursor cell	6.13e-11	57
myoblast	6.13e-11	57
multi-potent skeletal muscle stem cell	6.13e-11	57
contractile cell	1.46e-10	59
muscle cell	9.46e-10	54
electrically responsive cell	1.36e-09	60
electrically active cell	1.36e-09	60
preadipocyte	2.78e-09	12
skin fibroblast	1.66e-08	23
stromal cell	3.35e-08	27

Uber Anatomy

Ontology term	p-value	n
dermomyotome	6.64e-14	70
multilaminar epithelium	1.01e-12	82
somite	1.78e-12	83
paraxial mesoderm	1.78e-12	83
presomitic mesoderm	1.78e-12	83
presumptive segmental plate	1.78e-12	83
trunk paraxial mesoderm	1.78e-12	83
presumptive paraxial mesoderm	1.78e-12	83
muscle tissue	3.47e-11	63
musculature	3.47e-11	63
musculature of body	3.47e-11	63
skeletal muscle tissue	7.63e-11	61
striated muscle tissue	7.63e-11	61
myotome	7.63e-11	61
organism subdivision	7.64e-10	365
trunk mesenchyme	2.20e-09	143
integument	3.54e-08	45
integumental system	3.54e-08	45
trunk	3.55e-08	216
multi-cellular organism	1.78e-07	659

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
ZNF263#10127	7	3.19738285883749	0.00368052163702278	0.0185713595153649

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.