Coexpression cluster:C276

Full id: C276_mesothelioma_kidney_renal_small_clear_cerebellum_Renal

Phase1 CAGE Peaks

Hg19::chr10:34987954..34987974,-	p@chr10:34987954..34987974 -
Hg19::chr10:35013710..35013742,+	p@chr10:35013710..35013742 +
Hg19::chr12:127690461..127690477,-	p@chr12:127690461..127690477 -
Hg19::chr16:12071528..12071579,-	p@chr16:12071528..12071579 -
Hg19::chr16:12071607..12071614,-	p@chr16:12071607..12071614 -
Hg19::chr16:12071625..12071637,-	p@chr16:12071625..12071637 -
Hg19::chr16:12071655..12071667,-	p@chr16:12071655..12071667 -
Hg19::chr17:68130483..68130490,+	p@chr17:68130483..68130490 +
Hg19::chr18:8707570..8707590,-	p@chr18:8707570..8707590 -
Hg19::chr18:8707629..8707682,-	p@chr18:8707629..8707682 -
Hg19::chr19:21907110..21907113,+	p@chr19:21907110..21907113 +
Hg19::chr1:145727608..145727615,+	p13@PDZK1
Hg19::chr1:145727640..145727651,+	p5@PDZK1
Hg19::chr1:201178082..201178093,+	p@chr1:201178082..201178093 +
Hg19::chr1:51796987..51797001,-	p8@TTC39A
Hg19::chr1:62212760..62212775,+	p@chr1:62212760..62212775 +
Hg19::chr1:81001373..81001388,+	p2@ENST00000418041 p2@ENST00000443104
Hg19::chr1:81001398..81001426,+	p1@ENST00000418041 p1@ENST00000443104
Hg19::chr1:858638..858648,+	p@chr1:858638..858648 +
Hg19::chr1:874109..874143,+	p@chr1:874109..874143 +
Hg19::chr1:874201..874212,+	p8@SAMD11
Hg19::chr22:35779090..35779122,+	p9@HMOX1
Hg19::chr22:45072983..45072995,+	p9@PRR5
Hg19::chr2:191792376..191792426,+	p3@GLS
Hg19::chr2:234526272..234526280,+	p2@UGT1A8
Hg19::chr2:234526341..234526346,+	p1@UGT1A8
Hg19::chr3:19962031..19962047,-	p@chr3:19962031..19962047 -
Hg19::chr3:69812649..69812658,+	p20@MITF
Hg19::chr3:69812701..69812729,+	p9@MITF
Hg19::chr3:69812731..69812742,+	p19@MITF
Hg19::chr3:69812745..69812760,+	p10@MITF
Hg19::chr3:69812764..69812775,+	p18@MITF
Hg19::chr3:69812798..69812824,+	p8@MITF
Hg19::chr3:69812852..69812864,+	p17@MITF
Hg19::chr3:69812877..69812886,+	p22@MITF
Hg19::chr4:160521424..160521437,-	p@chr4:160521424..160521437 -
Hg19::chr4:23735183..23735192,-	p1@ENST00000507666
Hg19::chr5:13903866..13903886,-	p@chr5:13903866..13903886 -
Hg19::chr5:156485016..156485034,-	p3@HAVCR1
Hg19::chr5:168246378..168246386,+	p@chr5:168246378..168246386 +
Hg19::chr5:58806588..58806600,-	p@chr5:58806588..58806600 -
Hg19::chr7:107968921..107968937,-	p9@NRCAM
Hg19::chr7:107968952..107968990,-	p5@NRCAM
Hg19::chr7:107968999..107969017,-	p10@NRCAM
Hg19::chr9:119741711..119741743,-	p@chr9:119741711..119741743 -
Hg19::chrX:146262612..146262636,+	p@chrX:146262612..146262636 +
Hg19::chrX:41449223..41449229,-	p20@CASK

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:0043301	negative regulation of leukocyte degranulation	0.019335975245152
GO:0006543	glutamine catabolic process	0.019335975245152
GO:0045920	negative regulation of exocytosis	0.019335975245152
GO:0043305	negative regulation of mast cell degranulation	0.019335975245152
GO:0005124	scavenger receptor binding	0.019335975245152
GO:0032764	negative regulation of mast cell cytokine production	0.019335975245152
GO:0004392	heme oxygenase (decyclizing) activity	0.019335975245152
GO:0031670	cellular response to nutrient	0.019335975245152
GO:0006788	heme oxidation	0.019335975245152
GO:0045162	clustering of voltage-gated sodium channels	0.019335975245152
GO:0002701	negative regulation of production of molecular mediator of immune response	0.019335975245152
GO:0045666	positive regulation of neuron differentiation	0.019335975245152
GO:0042167	heme catabolic process	0.019335975245152
GO:0046149	pigment catabolic process	0.019335975245152
GO:0002719	negative regulation of cytokine production during immune response	0.019335975245152
GO:0005792	microsome	0.019335975245152
GO:0042598	vesicular fraction	0.019335975245152
GO:0032762	mast cell cytokine production	0.019335975245152
GO:0032763	regulation of mast cell cytokine production	0.019335975245152
GO:0043304	regulation of mast cell degranulation	0.019335975245152
GO:0002698	negative regulation of immune effector process	0.019335975245152
GO:0043300	regulation of leukocyte degranulation	0.0195193122881176
GO:0045161	neuronal ion channel clustering	0.0195193122881176
GO:0007413	axonal fasciculation	0.0195193122881176
GO:0006787	porphyrin catabolic process	0.0195193122881176
GO:0033015	tetrapyrrole catabolic process	0.0195193122881176
GO:0004359	glutaminase activity	0.0202973959740903
GO:0004630	phospholipase D activity	0.0202973959740903
GO:0030506	ankyrin binding	0.0202973959740903
GO:0043392	negative regulation of DNA binding	0.0202973959740903
GO:0043303	mast cell degranulation	0.021360020662496
GO:0002448	mast cell mediated immunity	0.021360020662496
GO:0051100	negative regulation of binding	0.021360020662496
GO:0045576	mast cell activation	0.021360020662496
GO:0043299	leukocyte degranulation	0.021360020662496
GO:0030318	melanocyte differentiation	0.021360020662496
GO:0045768	positive regulation of anti-apoptosis	0.021360020662496
GO:0050931	pigment cell differentiation	0.021360020662496
GO:0002718	regulation of cytokine production during immune response	0.0217385700965078
GO:0002700	regulation of production of molecular mediator of immune response	0.0217385700965078
GO:0002367	cytokine production during immune response	0.0217385700965078
GO:0002444	myeloid leukocyte mediated immunity	0.0217385700965078
GO:0002683	negative regulation of immune system process	0.0220507010573156
GO:0001818	negative regulation of cytokine production	0.0220507010573156
GO:0031669	cellular response to nutrient levels	0.0220507010573156
GO:0042551	neuron maturation	0.0220507010573156
GO:0051101	regulation of DNA binding	0.022767708270412
GO:0008038	neuron recognition	0.022767708270412
GO:0004385	guanylate kinase activity	0.022767708270412
GO:0045767	regulation of anti-apoptosis	0.02386032000429
GO:0030516	regulation of axon extension	0.02386032000429
GO:0031668	cellular response to extracellular stimulus	0.0272944817406109
GO:0002697	regulation of immune effector process	0.0281572440458984
GO:0017157	regulation of exocytosis	0.0281572440458984
GO:0048066	pigmentation during development	0.0289579016086571
GO:0043433	negative regulation of transcription factor activity	0.0289579016086571
GO:0015893	drug transport	0.0297028791663547
GO:0048675	axon extension	0.0297028791663547
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.0326260269476884
GO:0009065	glutamine family amino acid catabolic process	0.0326770919232935
GO:0030165	PDZ domain binding	0.0326770919232935
GO:0042168	heme metabolic process	0.0326770919232935
GO:0043627	response to estrogen stimulus	0.0353648820613477
GO:0051716	cellular response to stimulus	0.037595458508835
GO:0006541	glutamine metabolic process	0.037595458508835
GO:0051241	negative regulation of multicellular organismal process	0.037595458508835
GO:0007416	synaptogenesis	0.037595458508835
GO:0050770	regulation of axonogenesis	0.037595458508835
GO:0016599	caveolar membrane	0.037595458508835
GO:0045664	regulation of neuron differentiation	0.037595458508835
GO:0002440	production of molecular mediator of immune response	0.0379519283882688
GO:0002274	myeloid leukocyte activation	0.0379519283882688
GO:0051098	regulation of binding	0.0388132719405581
GO:0005901	caveola	0.0396509746626627
GO:0006778	porphyrin metabolic process	0.0404659822718011
GO:0051051	negative regulation of transport	0.041259190710588
GO:0015020	glucuronosyltransferase activity	0.0446465934736366
GO:0033013	tetrapyrrole metabolic process	0.0453644961172646
GO:0001764	neuron migration	0.0454880875821726
GO:0008629	induction of apoptosis by intracellular signals	0.0454880875821726
GO:0048545	response to steroid hormone stimulus	0.0457166616648321
GO:0050767	regulation of neurogenesis	0.0457166616648321
GO:0008037	cell recognition	0.0457166616648321
GO:0019201	nucleotide kinase activity	0.0457166616648321
GO:0050808	synapse organization and biogenesis	0.0463615983090679
GO:0001817	regulation of cytokine production	0.0477366896370438
GO:0007584	response to nutrient	0.0477366896370438
GO:0042440	pigment metabolic process	0.0477366896370438
GO:0042221	response to chemical stimulus	0.0477366896370438
GO:0042770	DNA damage response, signal transduction	0.0482512708214898
GO:0048469	cell maturation	0.0499274040431469

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>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
kidney	3.38e-12	26
kidney mesenchyme	3.38e-12	26
upper urinary tract	3.38e-12	26
kidney rudiment	3.38e-12	26
kidney field	3.38e-12	26
cavitated compound organ	2.36e-10	31
urinary system structure	4.59e-07	47
renal system	6.25e-07	48

Disease

Ontology term	p-value	n
clear cell adenocarcinoma	9.07e-18	2

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
NR3C1#2908	12	3.82289957391652	4.49857387869627e-05	0.000791620147122425

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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