Coexpression cluster:C323

Full id: C323_Placental_Amniotic_neuroblastoma_amniotic_chorionic_hairy_locus

Phase1 CAGE Peaks

Hg19::chr11:16893031..16893035,-	p@chr11:16893031..16893035 -
Hg19::chr11:16893073..16893090,-	p@chr11:16893073..16893090 -
Hg19::chr11:16947179..16947259,-	p@chr11:16947179..16947259 -
Hg19::chr11:2011185..2011202,-	p1@MRPL23-AS1
Hg19::chr11:2188016..2188030,-	p2@TH
Hg19::chr11:2193037..2193053,-	p1@TH
Hg19::chr12:120686548..120686582,-	p14@PXN
Hg19::chr14:104202639..104202646,-	p@chr14:104202639..104202646 -
Hg19::chr14:104202674..104202690,-	p@chr14:104202674..104202690 -
Hg19::chr14:69095369..69095386,-	p3@ENST00000556301
Hg19::chr16:3038260..3038264,+	p@chr16:3038260..3038264 +
Hg19::chr16:81679150..81679182,+	p17@CMIP
Hg19::chr16:81679223..81679271,+	p@chr16:81679223..81679271 +
Hg19::chr17:2278539..2278556,+	p6@SGSM2
Hg19::chr19:36592910..36592917,+	p@chr19:36592910..36592917 +
Hg19::chr1:114522973..114522995,+	p@chr1:114522973..114522995 +
Hg19::chr1:114523008..114523020,+	p@chr1:114523008..114523020 +
Hg19::chr1:147232729..147232730,-	p9@GJA5
Hg19::chr1:209704573..209704587,+	p@chr1:209704573..209704587 +
Hg19::chr1:209704612..209704625,+	p@chr1:209704612..209704625 +
Hg19::chr1:209704633..209704641,+	p@chr1:209704633..209704641 +
Hg19::chr1:209704648..209704656,+	p@chr1:209704648..209704656 +
Hg19::chr2:237682954..237682971,+	p@chr2:237682954..237682971 +
Hg19::chr2:237682972..237682977,+	p@chr2:237682972..237682977 +
Hg19::chr2:237682990..237683009,+	p@chr2:237682990..237683009 +
Hg19::chr2:237683020..237683029,+	p@chr2:237683020..237683029 +
Hg19::chr2:237683038..237683048,+	p@chr2:237683038..237683048 +
Hg19::chr2:237683109..237683120,+	p@chr2:237683109..237683120 +
Hg19::chr2:237683156..237683171,+	p@chr2:237683156..237683171 +
Hg19::chr2:237683203..237683210,+	p@chr2:237683203..237683210 +
Hg19::chr2:237683212..237683239,+	p@chr2:237683212..237683239 +
Hg19::chr3:55518443..55518474,-	p@chr3:55518443..55518474 -
Hg19::chr5:89143573..89143607,-	p@chr5:89143573..89143607 -
Hg19::chr7:29603266..29603282,-	p1@ENST00000447171 p1@uc003tab.2
Hg19::chr8:27995319..27995365,+	p@chr8:27995319..27995365 +
Hg19::chr9:88126069..88126080,-	p@chr9:88126069..88126080 -

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:0004511	tyrosine 3-monooxygenase activity	0.0237309072152451
GO:0017166	vinculin binding	0.0237309072152451
GO:0006461	protein complex assembly	0.0237309072152451
GO:0007154	cell communication	0.0237309072152451
GO:0035050	embryonic heart tube development	0.0237309072152451
GO:0042423	catecholamine biosynthetic process	0.0240901397280719
GO:0016714	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen	0.0240901397280719
GO:0007043	intercellular junction assembly	0.0240901397280719
GO:0042136	neurotransmitter biosynthetic process	0.0240901397280719
GO:0007172	signal complex assembly	0.0240901397280719
GO:0045216	intercellular junction assembly and maintenance	0.0240901397280719
GO:0007028	cytoplasm organization and biogenesis	0.0240901397280719
GO:0065003	macromolecular complex assembly	0.0240901397280719
GO:0006584	catecholamine metabolic process	0.0240901397280719
GO:0018958	phenol metabolic process	0.0240901397280719
GO:0005922	connexon complex	0.0240901397280719
GO:0022607	cellular component assembly	0.0240901397280719
GO:0042133	neurotransmitter metabolic process	0.0240901397280719
GO:0030326	embryonic limb morphogenesis	0.0240901397280719
GO:0035113	embryonic appendage morphogenesis	0.0240901397280719
GO:0005921	gap junction	0.0240901397280719
GO:0042401	biogenic amine biosynthetic process	0.0240901397280719
GO:0060173	limb development	0.0240901397280719
GO:0035107	appendage morphogenesis	0.0240901397280719
GO:0035108	limb morphogenesis	0.0240901397280719
GO:0048736	appendage development	0.0240901397280719
GO:0042398	amino acid derivative biosynthetic process	0.0263269511231556
GO:0009653	anatomical structure morphogenesis	0.0265091461685086
GO:0014704	intercalated disc	0.0265091461685086
GO:0009072	aromatic amino acid family metabolic process	0.0265091461685086
GO:0043623	cellular protein complex assembly	0.0376256946416683
GO:0006576	biogenic amine metabolic process	0.0390825555738343
GO:0001505	regulation of neurotransmitter levels	0.0399397314359315
GO:0006575	amino acid derivative metabolic process	0.0439818193873885
GO:0048598	embryonic morphogenesis	0.0439818193873885
GO:0007507	heart development	0.0439818193873885
GO:0003008	system process	0.0439818193873885
GO:0007160	cell-matrix adhesion	0.0439818193873885
GO:0031589	cell-substrate adhesion	0.0445776803648569
GO:0035295	tube development	0.0472129969561992
GO:0009309	amine biosynthetic process	0.0472129969561992
GO:0032313	regulation of Rab GTPase activity	0.0472129969561992
GO:0032483	regulation of Rab protein signal transduction	0.0472129969561992
GO:0032482	Rab protein signal transduction	0.0472129969561992
GO:0005097	Rab GTPase activator activity	0.0472129969561992

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
epithelial cell	1.18e-10	254

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	1.17e-12	347
organ part	3.38e-12	219
organism subdivision	1.47e-11	365
multi-cellular organism	1.72e-10	659
ectoderm-derived structure	2.43e-10	169
endoderm-derived structure	2.50e-10	169
endoderm	2.50e-10	169
presumptive endoderm	2.50e-10	169
ectoderm	4.04e-10	173
presumptive ectoderm	4.04e-10	173
organ	9.13e-10	511
subdivision of digestive tract	9.24e-09	129
endodermal part of digestive tract	9.24e-09	129
digestive system	2.11e-08	155
digestive tract	2.11e-08	155
primitive gut	2.11e-08	155
extraembryonic membrane	3.73e-08	14
membranous layer	3.73e-08	14
mixed endoderm/mesoderm-derived structure	1.14e-07	130
anatomical system	1.40e-07	625
adult organism	2.11e-07	115
mesenchyme	2.15e-07	238
entire embryonic mesenchyme	2.15e-07	238
anatomical group	2.29e-07	626
embryo	6.72e-07	612
internal genitalia	7.50e-07	25

Disease

Ontology term	p-value	n
cell type cancer	4.10e-09	143
carcinoma	9.53e-09	106

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	7	2.91142120328365	0.00886219771266859	0.033626124138543

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.