Coexpression cluster:C1324

Full id: C1324_Fibroblast_Preadipocyte_basal_migratory_mesenchymal_Smooth_spindle

Phase1 CAGE Peaks

Hg19::chr10:95242223..95242232,-	p8@MYOF
Hg19::chr18:56246303..56246344,-	p9@ALPK2
Hg19::chr18:56246346..56246375,-	p6@ALPK2
Hg19::chr18:56246399..56246415,-	p15@ALPK2
Hg19::chr18:56246464..56246503,-	p3@ALPK2
Hg19::chr4:77659857..77659874,+	p3@SHROOM3

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:0043476	pigment accumulation	0.00447414122204642
GO:0043482	cellular pigment accumulation	0.00447414122204642
GO:0033059	cellular pigmentation	0.00447414122204642
GO:0045176	apical protein localization	0.00894736048387635
GO:0008105	asymmetric protein localization	0.00894736048387635
GO:0022603	regulation of anatomical structure morphogenesis	0.0234757577475775
GO:0008360	regulation of cell shape	0.0234757577475775
GO:0022604	regulation of cell morphogenesis	0.0234757577475775
GO:0005912	adherens junction	0.026824695916118
GO:0016324	apical plasma membrane	0.030395052708795
GO:0045177	apical part of cell	0.0349369160994711
GO:0007389	pattern specification process	0.0461504527999066

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	2.50e-25	180
fibroblast	7.41e-20	75
skin fibroblast	1.11e-11	23
muscle precursor cell	1.54e-08	57
myoblast	1.54e-08	57
multi-potent skeletal muscle stem cell	1.54e-08	57
smooth muscle cell	9.98e-08	42
smooth muscle myoblast	9.98e-08	42
preadipocyte	1.40e-07	12
muscle cell	1.56e-07	54
mesodermal cell	3.29e-07	119
contractile cell	4.20e-07	59
mesothelial cell	5.38e-07	19

Uber Anatomy

Ontology term	p-value	n
somite	1.20e-12	83
paraxial mesoderm	1.20e-12	83
presomitic mesoderm	1.20e-12	83
presumptive segmental plate	1.20e-12	83
trunk paraxial mesoderm	1.20e-12	83
presumptive paraxial mesoderm	1.20e-12	83
trunk mesenchyme	4.92e-12	143
dermomyotome	1.66e-11	70
trunk	4.14e-11	216
mesoderm	1.38e-10	448
mesoderm-derived structure	1.38e-10	448
presumptive mesoderm	1.38e-10	448
integument	3.53e-10	45
integumental system	3.53e-10	45
surface structure	7.22e-10	95
muscle tissue	1.18e-09	63
musculature	1.18e-09	63
musculature of body	1.18e-09	63
multilaminar epithelium	1.83e-09	82
skeletal muscle tissue	3.23e-09	61
striated muscle tissue	3.23e-09	61
myotome	3.23e-09	61
skin of body	3.56e-09	40
mesenchyme	4.77e-09	238
entire embryonic mesenchyme	4.77e-09	238
multi-cellular organism	4.03e-08	659
organism subdivision	7.56e-08	365
anatomical system	1.47e-07	625
anatomical group	2.26e-07	626
organ component layer	6.30e-07	57

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
STAT3#6774	5	8.76622083096187	4.28672496720299e-05	0.000765955977501647

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.