Coexpression cluster:C4804

Full id: C4804_Placental_amniotic_Smooth_chorionic_Amniotic_Mesothelial_Fibroblast

Phase1 CAGE Peaks

Hg19::chr9:132515289..132515300,-	p3@PTGES
Hg19::chr9:132515302..132515338,-	p1@PTGES
Hg19::chr9:132515340..132515357,-	p2@PTGES

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	1.25e-14	180
muscle precursor cell	5.55e-08	57
myoblast	5.55e-08	57
multi-potent skeletal muscle stem cell	5.55e-08	57
muscle cell	6.64e-08	54
contractile cell	3.21e-07	59
fibroblast	3.91e-07	75

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	2.79e-14	659
multi-tissue structure	1.72e-13	347
mesenchyme	2.87e-12	238
entire embryonic mesenchyme	2.87e-12	238
organ component layer	4.77e-12	57
organism subdivision	5.36e-12	365
organ	5.37e-12	511
trunk	1.23e-11	216
anatomical system	1.41e-11	625
anatomical group	2.34e-11	626
surface structure	5.08e-10	95
multilaminar epithelium	7.77e-10	82
organ part	1.02e-09	219
extraembryonic membrane	1.51e-09	14
membranous layer	1.51e-09	14
germ layer	1.54e-09	604
embryonic tissue	1.54e-09	604
presumptive structure	1.54e-09	604
epiblast (generic)	1.54e-09	604
embryonic structure	1.76e-09	605
developing anatomical structure	1.76e-09	605
embryo	2.84e-09	612
trunk mesenchyme	2.97e-09	143
somite	5.43e-09	83
paraxial mesoderm	5.43e-09	83
presomitic mesoderm	5.43e-09	83
presumptive segmental plate	5.43e-09	83
trunk paraxial mesoderm	5.43e-09	83
presumptive paraxial mesoderm	5.43e-09	83
dermomyotome	1.29e-08	70
endoderm-derived structure	1.41e-08	169
endoderm	1.41e-08	169
presumptive endoderm	1.41e-08	169
mesoderm	1.71e-08	448
mesoderm-derived structure	1.71e-08	448
presumptive mesoderm	1.71e-08	448
subdivision of head	1.92e-08	48
skeletal muscle tissue	2.88e-07	61
striated muscle tissue	2.88e-07	61
myotome	2.88e-07	61
muscle tissue	3.43e-07	63
musculature	3.43e-07	63
musculature of body	3.43e-07	63
digestive system	4.76e-07	155
digestive tract	4.76e-07	155
primitive gut	4.76e-07	155
orifice	9.76e-07	35

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	3	4.98817909481014	0.00805648813738344	0.0322862347791792
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.012883791263738
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187584672781032
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0296430263990033
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00669369403595088
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249783524340474
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00619524273658835

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.