Coexpression cluster:C1960

Full id: C1960_Mesenchymal_Smooth_cholangiocellular_hepatic_bile_Fibroblast_mesenchymal

Phase1 CAGE Peaks

Hg19::chr5:33892081..33892101,-	p1@ADAMTS12
Hg19::chr5:33892102..33892117,-	p3@ADAMTS12
Hg19::chr5:33892118..33892144,-	p2@ADAMTS12
Hg19::chr5:33892167..33892190,-	p4@ADAMTS12
Hg19::chr5:33892204..33892218,-	p6@ADAMTS12

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	3.47e-40	180
muscle cell	4.49e-24	54
contractile cell	9.55e-24	59
muscle precursor cell	1.29e-23	57
myoblast	1.29e-23	57
multi-potent skeletal muscle stem cell	1.29e-23	57
electrically responsive cell	3.65e-23	60
electrically active cell	3.65e-23	60
smooth muscle cell	1.57e-20	42
smooth muscle myoblast	1.57e-20	42
fibroblast	9.95e-20	75
vascular associated smooth muscle cell	2.78e-17	32
mesodermal cell	3.59e-15	119
cardiocyte	1.49e-08	16
aortic smooth muscle cell	3.06e-07	10
preadipocyte	3.67e-07	12
fat cell	9.89e-07	15

Uber Anatomy

Ontology term	p-value	n
somite	8.43e-25	83
paraxial mesoderm	8.43e-25	83
presomitic mesoderm	8.43e-25	83
presumptive segmental plate	8.43e-25	83
trunk paraxial mesoderm	8.43e-25	83
presumptive paraxial mesoderm	8.43e-25	83
dermomyotome	1.02e-24	70
skeletal muscle tissue	7.77e-24	61
striated muscle tissue	7.77e-24	61
myotome	7.77e-24	61
muscle tissue	1.69e-23	63
musculature	1.69e-23	63
musculature of body	1.69e-23	63
trunk mesenchyme	4.03e-21	143
multilaminar epithelium	3.53e-20	82
organism subdivision	3.35e-16	365
trunk	3.61e-15	216
splanchnic layer of lateral plate mesoderm	8.76e-15	84
unilaminar epithelium	1.18e-13	138
vasculature	4.89e-13	79
vascular system	4.89e-13	79
cell layer	5.47e-13	312
epithelial tube	2.26e-12	118
epithelium	3.03e-12	309
multi-tissue structure	2.49e-11	347
cardiovascular system	3.57e-11	110
circulatory system	6.16e-11	113
artery	8.70e-11	42
arterial blood vessel	8.70e-11	42
arterial system	8.70e-11	42
systemic artery	2.77e-10	33
systemic arterial system	2.77e-10	33
blood vessel	1.18e-09	60
epithelial tube open at both ends	1.18e-09	60
blood vasculature	1.18e-09	60
vascular cord	1.18e-09	60
mesenchyme	5.34e-09	238
entire embryonic mesenchyme	5.34e-09	238
vessel	1.04e-08	69
heart	2.00e-08	24
primitive heart tube	2.00e-08	24
primary heart field	2.00e-08	24
anterior lateral plate mesoderm	2.00e-08	24
heart tube	2.00e-08	24
heart primordium	2.00e-08	24
cardiac mesoderm	2.00e-08	24
cardiogenic plate	2.00e-08	24
heart rudiment	2.00e-08	24
smooth muscle tissue	5.53e-08	15
primary circulatory organ	1.17e-07	27
blood vessel smooth muscle	3.06e-07	10
arterial system smooth muscle	3.06e-07	10
artery smooth muscle tissue	3.06e-07	10
aorta smooth muscle tissue	3.06e-07	10
anatomical cluster	3.34e-07	286
primordium	5.89e-07	168

Disease

Ontology term	p-value	n
ovarian cancer	2.27e-07	14

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
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00331059051976592

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.