Coexpression cluster:C1280

Full id: C1280_Preadipocyte_Fibroblast_Adipocyte_leiomyoblastoma_Ewing_Chondrocyte_spindle

Phase1 CAGE Peaks

Hg19::chr6:75787895..75787900,-	p@chr6:75787895..75787900 -
Hg19::chr6:75794459..75794475,-	p2@AL359627
Hg19::chr6:75886595..75886610,-	p@chr6:75886595..75886610 -
Hg19::chr6:75912479..75912515,+	p@chr6:75912479..75912515 +
Hg19::chr6:75915738..75915749,-	p2@COL12A1
Hg19::chr6:75915757..75915775,-	p1@COL12A1
Hg19::chr6:75915872..75915881,-	p3@COL12A1

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:0005595	collagen type XII	0.00100082420817143
GO:0030020	extracellular matrix structural constituent conferring tensile strength	0.00100082420817144
GO:0005593	FACIT collagen	0.00200164841634287
GO:0030934	anchoring collagen	0.00200164841634287
GO:0030199	collagen fibril organization	0.00200164841634287
GO:0030198	extracellular matrix organization and biogenesis	0.007672985595981
GO:0005581	collagen	0.00772064389160821
GO:0043062	extracellular structure organization and biogenesis	0.0105086541858001
GO:0005201	extracellular matrix structural constituent	0.0130107147062286
GO:0044420	extracellular matrix part	0.0130107147062286
GO:0006817	phosphate transport	0.0130107147062286
GO:0001501	skeletal development	0.0174310216256525
GO:0015698	inorganic anion transport	0.0200164841634287
GO:0006820	anion transport	0.0230904442313838
GO:0005578	proteinaceous extracellular matrix	0.0280897994426783

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	1.04e-27	180
fibroblast	2.41e-20	75
skin fibroblast	3.96e-10	23
muscle precursor cell	9.13e-09	57
myoblast	9.13e-09	57
multi-potent skeletal muscle stem cell	9.13e-09	57
muscle cell	2.29e-08	54
contractile cell	4.25e-08	59
fat cell	7.87e-08	15
electrically responsive cell	4.64e-07	60
electrically active cell	4.64e-07	60
stromal cell	8.52e-07	27

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.26e-18	365
multi-tissue structure	1.51e-14	347
surface structure	1.56e-14	95
multi-cellular organism	5.83e-14	659
somite	1.29e-13	83
paraxial mesoderm	1.29e-13	83
presomitic mesoderm	1.29e-13	83
presumptive segmental plate	1.29e-13	83
trunk paraxial mesoderm	1.29e-13	83
presumptive paraxial mesoderm	1.29e-13	83
trunk mesenchyme	1.98e-12	143
trunk	2.91e-12	216
dermomyotome	1.00e-10	70
mesenchyme	1.86e-10	238
entire embryonic mesenchyme	1.86e-10	238
multilaminar epithelium	2.01e-10	82
anatomical system	4.64e-10	625
anatomical group	8.17e-10	626
muscle tissue	9.66e-10	63
musculature	9.66e-10	63
musculature of body	9.66e-10	63
organ	1.34e-09	511
skeletal muscle tissue	1.49e-09	61
striated muscle tissue	1.49e-09	61
myotome	1.49e-09	61
integument	2.78e-09	45
integumental system	2.78e-09	45
skin of body	1.77e-08	40
organ component layer	2.03e-08	57
organ part	5.71e-07	219

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
BRCA1#672	3	8.65038456138161	0.00365929333120223	0.018475848983197
CTBP2#1488	3	26.8787144311406	0.000135090303129668	0.00177044750515239
GTF2F1#2962	3	5.45985466146756	0.013298821684157	0.0470276846303133
JUN#3725	3	5.36264108242986	0.0139726108558902	0.0490582096812451
SMARCB1#6598	3	7.8225924776389	0.00486874272566658	0.0227847211330327
SMARCC1#6599	3	18.7128682798421	0.000392094926695795	0.0038353471995113
TFAP2A#7020	3	7.07941473130498	0.00645255447218097	0.028032376727126
TRIM28#10155	3	7.96736787654108	0.00462234126315646	0.0218341338391134

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.