Coexpression cluster:C2574

Full id: C2574_Mesenchymal_Pericytes_Fibroblast_Adipocyte_Nucleus_Meningeal_stomach

Phase1 CAGE Peaks

Hg19::chr1:236228379..236228402,-	p1@NID1
Hg19::chr1:236228403..236228414,-	p3@NID1
Hg19::chr1:236228417..236228446,-	p2@NID1
Hg19::chr1:236228490..236228507,-	p4@NID1

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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No GOStat results

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	2.60e-27	180
fibroblast	7.39e-18	75
mesodermal cell	1.31e-15	119
contractile cell	5.37e-11	59
muscle precursor cell	5.50e-10	57
myoblast	5.50e-10	57
multi-potent skeletal muscle stem cell	5.50e-10	57
muscle cell	2.35e-09	54
endothelial cell	8.70e-09	35
skin fibroblast	1.89e-08	23
meso-epithelial cell	3.55e-08	44
electrically responsive cell	5.31e-08	60
electrically active cell	5.31e-08	60
fat cell	1.54e-07	15
endothelial cell of vascular tree	1.81e-07	24

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	5.88e-17	659
trunk mesenchyme	1.03e-16	143
vasculature	2.84e-14	79
vascular system	2.84e-14	79
unilaminar epithelium	3.67e-14	138
epithelial tube	4.43e-13	118
trunk	1.22e-12	216
organism subdivision	1.27e-12	365
anatomical system	1.33e-12	625
somite	1.51e-12	83
paraxial mesoderm	1.51e-12	83
presomitic mesoderm	1.51e-12	83
presumptive segmental plate	1.51e-12	83
trunk paraxial mesoderm	1.51e-12	83
presumptive paraxial mesoderm	1.51e-12	83
dermomyotome	2.50e-12	70
anatomical group	2.65e-12	626
circulatory system	3.48e-12	113
splanchnic layer of lateral plate mesoderm	3.66e-12	84
cardiovascular system	1.72e-11	110
muscle tissue	2.87e-11	63
musculature	2.87e-11	63
musculature of body	2.87e-11	63
multilaminar epithelium	4.08e-11	82
cell layer	5.72e-11	312
skeletal muscle tissue	6.27e-11	61
striated muscle tissue	6.27e-11	61
myotome	6.27e-11	61
vessel	1.04e-10	69
epithelium	4.02e-10	309
anatomical cluster	1.16e-08	286
blood vessel	2.29e-08	60
epithelial tube open at both ends	2.29e-08	60
blood vasculature	2.29e-08	60
vascular cord	2.29e-08	60
multi-tissue structure	3.07e-08	347
mesoderm	8.33e-08	448
mesoderm-derived structure	8.33e-08	448
presumptive mesoderm	8.33e-08	448
abdominal segment of trunk	1.63e-07	61
abdomen	1.63e-07	61
anatomical conduit	2.74e-07	241
embryo	5.30e-07	612
mesenchyme	8.86e-07	238
entire embryonic mesenchyme	8.86e-07	238

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
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00817810903946973
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186206370427919
HNF4A#3172	4	23.1322903629537	3.48990320893214e-06	0.000115671850599068
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322471319174445
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244474676300832
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106922342713081
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249126775259601

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.