Coexpression cluster:C39

Full id: C39_epididymis_ductus_seminal_testis_acute_thyroid_CD133

Phase1 CAGE Peaks

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Hg19::chr10:102488968..102488983,+	p@chr10:102488968..102488983 +
Hg19::chr10:102502448..102502455,+	p@chr10:102502448..102502455 +
Hg19::chr10:102502483..102502493,+	p@chr10:102502483..102502493 +
Hg19::chr10:102502638..102502642,+	p@chr10:102502638..102502642 +
Hg19::chr10:102505312..102505320,+	p6@PAX2
Hg19::chr10:102505327..102505344,+	p1@PAX2
Hg19::chr10:102505552..102505563,+	p5@PAX2
Hg19::chr10:102505655..102505689,+	p10@PAX2
Hg19::chr10:102505901..102505907,+	p13@PAX2
Hg19::chr10:102543435..102543439,+	p@chr10:102543435..102543439 +
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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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GO ID	GO name	FDR corrected p-value
GO:0042742	defense response to bacterium	2.57358103660875e-17
GO:0009617	response to bacterium	5.75568533087663e-17
GO:0051707	response to other organism	2.65519661258531e-13
GO:0009607	response to biotic stimulus	1.5706494034578e-11
GO:0051704	multi-organism process	7.6126961140875e-11
GO:0006952	defense response	5.21198666657427e-09
GO:0030414	protease inhibitor activity	8.34111943821792e-07
GO:0004866	endopeptidase inhibitor activity	7.59444133361891e-06
GO:0004867	serine-type endopeptidase inhibitor activity	7.59444133361891e-06
GO:0004857	enzyme inhibitor activity	1.92678201597427e-05
GO:0004522	pancreatic ribonuclease activity	0.00103973182225395
GO:0016892	endoribonuclease activity, producing 3'-phosphomonoesters	0.00174869510084071
GO:0016894	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	0.00199396234918022
GO:0006629	lipid metabolic process	0.00231003462070621
GO:0019953	sexual reproduction	0.00328427593768674
GO:0007338	single fertilization	0.0106024648605205
GO:0009566	fertilization	0.0110716057967754
GO:0004519	endonuclease activity	0.0130618980962842
GO:0004521	endoribonuclease activity	0.0187160920694898
GO:0007283	spermatogenesis	0.0375243664717349
GO:0048232	male gamete generation	0.0375243664717349
GO:0004540	ribonuclease activity	0.0375243664717349
GO:0045087	innate immune response	0.0375243664717349
GO:0051149	positive regulation of muscle cell differentiation	0.0375243664717349
GO:0004617	phosphoglycerate dehydrogenase activity	0.0375243664717349
GO:0005982	starch metabolic process	0.0375243664717349
GO:0043416	regulation of skeletal muscle regeneration	0.0375243664717349
GO:0019747	regulation of isoprenoid metabolic process	0.0375243664717349
GO:0015633	zinc transporting ATPase activity	0.0375243664717349
GO:0004608	phosphatidylethanolamine N-methyltransferase activity	0.0375243664717349
GO:0005983	starch catabolic process	0.0375243664717349
GO:0051155	positive regulation of striated muscle cell differentiation	0.0375243664717349
GO:0043415	positive regulation of skeletal muscle regeneration	0.0375243664717349
GO:0009917	sterol 5-alpha reductase activity	0.0375243664717349
GO:0051153	regulation of striated muscle cell differentiation	0.0375243664717349
GO:0004518	nuclease activity	0.0386689632252155
GO:0005184	neuropeptide hormone activity	0.0401226071427917
GO:0007276	gamete generation	0.0472744431405105
GO:0006810	transport	0.0479396339481545

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
male genital duct	1.71e-66	3
internal male genitalia	1.71e-66	3
epididymis	1.46e-50	1
vas deferens	2.42e-50	1
spermatic cord	2.42e-50	1
duct of male reproductive system	3.11e-50	4
male reproductive organ	4.07e-41	11
male organism	3.99e-21	22
male reproductive system	3.99e-21	22
duct	1.55e-11	19
reproductive organ	3.32e-10	48
internal genitalia	5.06e-09	25
reproductive structure	1.83e-08	59
reproductive system	1.83e-08	59
mesonephric epithelium	1.49e-07	8
mesonephric tubule	1.49e-07	8
nephric duct	1.49e-07	8
renal duct	1.49e-07	8
mesonephric duct	1.49e-07	8
pronephric duct	1.49e-07	8
testis	1.69e-07	8
mesonephros	7.48e-07	9
pronephros	7.48e-07	9
nephrogenic cord	7.48e-07	9
pronephric mesoderm	7.48e-07	9
rostral part of nephrogenic cord	7.48e-07	9
presumptive pronephric mesoderm	7.48e-07	9

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
ESR1#2099	28	1.87287150498332	0.00133367099868708	0.00885206643990338

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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FF samples	Score

FF samples	Score
epididymis, adult CNhs12847	1.10
ductus deferens, adult CNhs12846	0.25
testis, adult, pool1 CNhs10632	0.09
Clontech Human Universal Reference Total RNA, pool1 CNhs10608	0.03
Adipocyte - breast, donor1 CNhs11051	0.00
Adipocyte - breast, donor2 CNhs11969	0.00
Adipocyte - omental, donor1 CNhs11054	0.00
Adipocyte - omental, donor2 CNhs12067	0.00
Adipocyte - omental, donor3 CNhs12068	0.00
Adipocyte - perirenal, donor1 CNhs12069	0.00

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