Coexpression cluster:C471

Full id: C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate

Phase1 CAGE Peaks

Hg19::chr8:42033234..42033247,-	p@chr8:42033234..42033247 -
Hg19::chr8:42033253..42033264,-	p@chr8:42033253..42033264 -
Hg19::chr8:42033364..42033376,-	p@chr8:42033364..42033376 -
Hg19::chr8:42033383..42033398,-	p@chr8:42033383..42033398 -
Hg19::chr8:42033546..42033576,-	p@chr8:42033546..42033576 -
Hg19::chr8:42033578..42033605,-	p@chr8:42033578..42033605 -
Hg19::chr8:42033607..42033639,-	p@chr8:42033607..42033639 -
Hg19::chr8:42033640..42033671,-	p@chr8:42033640..42033671 -
Hg19::chr8:42036444..42036460,+	p@chr8:42036444..42036460 +
Hg19::chr8:42036539..42036561,-	p@chr8:42036539..42036561 -
Hg19::chr8:42037500..42037536,-	p@chr8:42037500..42037536 -
Hg19::chr8:42037883..42037900,-	p@chr8:42037883..42037900 -
Hg19::chr8:42038055..42038068,-	p3@PLAT
Hg19::chr8:42040287..42040298,-	p10@PLAT
Hg19::chr8:42042635..42042650,-	p4@PLAT
Hg19::chr8:42042654..42042665,-	p9@PLAT
Hg19::chr8:42044953..42044969,-	p@chr8:42044953..42044969 -
Hg19::chr8:42044977..42044996,-	p@chr8:42044977..42044996 -
Hg19::chr8:42045498..42045512,-	p6@PLAT
Hg19::chr8:42065075..42065090,-	p1@PLAT
Hg19::chr8:42065187..42065201,-	p2@PLAT

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	6.24e-27	180
contractile cell	4.88e-23	59
muscle precursor cell	1.13e-21	57
myoblast	1.13e-21	57
multi-potent skeletal muscle stem cell	1.13e-21	57
muscle cell	5.62e-21	54
smooth muscle cell	2.16e-20	42
smooth muscle myoblast	2.16e-20	42
mesodermal cell	5.75e-20	119
electrically responsive cell	8.61e-19	60
electrically active cell	8.61e-19	60
vascular associated smooth muscle cell	3.90e-16	32
embryonic cell	4.67e-15	248
fibroblast	1.35e-11	75
epithelial cell of nephron	7.93e-08	16
kidney tubule cell	2.37e-07	12
nephron tubule epithelial cell	2.37e-07	12
aortic smooth muscle cell	4.25e-07	10

Uber Anatomy

Ontology term	p-value	n
cell layer	4.09e-29	312
epithelium	2.46e-28	309
organism subdivision	3.16e-26	365
trunk mesenchyme	5.16e-26	143
multi-tissue structure	2.61e-23	347
somite	1.36e-22	83
paraxial mesoderm	1.36e-22	83
presomitic mesoderm	1.36e-22	83
presumptive segmental plate	1.36e-22	83
trunk paraxial mesoderm	1.36e-22	83
presumptive paraxial mesoderm	1.36e-22	83
multi-cellular organism	5.09e-22	659
epithelial tube	9.33e-22	118
dermomyotome	1.55e-21	70
multilaminar epithelium	3.04e-21	82
vasculature	3.55e-21	79
vascular system	3.55e-21	79
muscle tissue	5.40e-21	63
musculature	5.40e-21	63
musculature of body	5.40e-21	63
anatomical system	1.02e-20	625
skeletal muscle tissue	1.40e-20	61
striated muscle tissue	1.40e-20	61
myotome	1.40e-20	61
anatomical group	1.58e-20	626
splanchnic layer of lateral plate mesoderm	3.26e-20	84
trunk	3.72e-20	216
anatomical conduit	1.43e-19	241
anatomical cluster	3.48e-19	286
artery	2.03e-18	42
arterial blood vessel	2.03e-18	42
arterial system	2.03e-18	42
blood vessel	4.02e-18	60
epithelial tube open at both ends	4.02e-18	60
blood vasculature	4.02e-18	60
vascular cord	4.02e-18	60
vessel	2.31e-17	69
embryo	3.77e-17	612
embryonic structure	4.85e-17	605
developing anatomical structure	4.85e-17	605
germ layer	9.13e-17	604
embryonic tissue	9.13e-17	604
presumptive structure	9.13e-17	604
epiblast (generic)	9.13e-17	604
systemic artery	1.83e-16	33
systemic arterial system	1.83e-16	33
unilaminar epithelium	1.89e-16	138
tube	2.14e-15	194
cardiovascular system	1.58e-14	110
circulatory system	3.20e-14	113
mesenchyme	1.97e-13	238
entire embryonic mesenchyme	1.97e-13	238
compound organ	4.19e-11	69
aorta	1.24e-09	21
aortic system	1.24e-09	21
intermediate mesoderm	2.03e-09	37
urogenital ridge	3.69e-09	20
smooth muscle tissue	4.78e-09	15
organ	1.02e-08	511
mesonephros	2.67e-08	18
pronephros	2.67e-08	18
nephrogenic cord	2.67e-08	18
pronephric mesoderm	2.67e-08	18
rostral part of nephrogenic cord	2.67e-08	18
presumptive pronephric mesoderm	2.67e-08	18
excretory tube	3.55e-08	17
mesonephric epithelium	3.55e-08	17
mesonephric tubule	3.55e-08	17
nephric duct	3.55e-08	17
kidney epithelium	3.55e-08	17
renal duct	3.55e-08	17
mesonephric duct	3.55e-08	17
pronephric duct	3.55e-08	17
organ part	6.05e-08	219
nephron epithelium	7.93e-08	16
nephron	7.93e-08	16
uriniferous tubule	7.93e-08	16
metanephric mesenchyme	7.93e-08	16
nephrogenic mesenchyme	7.93e-08	16
mesoderm	1.61e-07	448

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
MEF2C#4208	3	5.90162207037486	0.0136071743920147	0.048017289036614

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.