Coexpression cluster:C3029

Full id: C3029_Cardiac_tridermal_sacrococcigeal_mesothelioma_endometrial_tenocyte_Fibroblast

Phase1 CAGE Peaks

Hg19::chr10:60272624..60272640,+	p1@BICC1
Hg19::chr10:60272743..60272754,+	p4@BICC1
Hg19::chr10:60272814..60272831,+	p2@BICC1

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	6.67e-32	180
fibroblast	1.27e-18	75
muscle precursor cell	7.41e-14	57
myoblast	7.41e-14	57
multi-potent skeletal muscle stem cell	7.41e-14	57
contractile cell	3.82e-13	59
muscle cell	5.03e-13	54
electrically responsive cell	5.28e-11	60
electrically active cell	5.28e-11	60
smooth muscle cell	7.41e-10	42
smooth muscle myoblast	7.41e-10	42
vascular associated smooth muscle cell	3.27e-09	32
cardiocyte	8.09e-08	16

Uber Anatomy

Ontology term	p-value	n
organism subdivision	6.01e-21	365
multi-tissue structure	1.19e-20	347
trunk mesenchyme	1.30e-20	143
mesenchyme	3.05e-17	238
entire embryonic mesenchyme	3.05e-17	238
somite	3.17e-17	83
paraxial mesoderm	3.17e-17	83
presomitic mesoderm	3.17e-17	83
presumptive segmental plate	3.17e-17	83
trunk paraxial mesoderm	3.17e-17	83
presumptive paraxial mesoderm	3.17e-17	83
trunk	4.31e-17	216
dermomyotome	1.52e-15	70
multilaminar epithelium	2.70e-15	82
skeletal muscle tissue	6.37e-15	61
striated muscle tissue	6.37e-15	61
myotome	6.37e-15	61
muscle tissue	1.21e-14	63
musculature	1.21e-14	63
musculature of body	1.21e-14	63
multi-cellular organism	1.28e-14	659
anatomical system	2.78e-13	625
anatomical group	5.22e-13	626
cell layer	2.80e-12	312
compound organ	5.29e-12	69
epithelium	7.73e-12	309
anatomical cluster	2.07e-10	286
epithelial tube	5.66e-10	118
embryonic structure	8.56e-10	605
developing anatomical structure	8.56e-10	605
surface structure	9.34e-10	95
heart	1.03e-09	24
primitive heart tube	1.03e-09	24
primary heart field	1.03e-09	24
anterior lateral plate mesoderm	1.03e-09	24
heart tube	1.03e-09	24
heart primordium	1.03e-09	24
cardiac mesoderm	1.03e-09	24
cardiogenic plate	1.03e-09	24
heart rudiment	1.03e-09	24
germ layer	1.25e-09	604
embryonic tissue	1.25e-09	604
presumptive structure	1.25e-09	604
epiblast (generic)	1.25e-09	604
primary circulatory organ	1.39e-09	27
embryo	2.32e-09	612
organ	5.38e-09	511
tissue	9.20e-08	787
unilaminar epithelium	2.39e-07	138
mesoderm	2.65e-07	448
mesoderm-derived structure	2.65e-07	448
presumptive mesoderm	2.65e-07	448
systemic artery	3.55e-07	33
systemic arterial system	3.55e-07	33
anatomical cavity	4.16e-07	70
body cavity precursor	4.36e-07	63

Disease

Ontology term	p-value	n
ovarian cancer	8.75e-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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0278194458787943
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323411356249436
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189438805115438

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.