Coexpression cluster:C981

Full id: C981_choriocarcinoma_chorionic_pancreatic_placenta_amniotic_vagina_MCF7

Phase1 CAGE Peaks

Hg19::chr10:71098164..71098182,+	p@chr10:71098164..71098182 +
Hg19::chr10:8097468..8097478,+	p16@GATA3
Hg19::chr1:161059803..161059816,-	p7@PVRL4
Hg19::chr1:161059882..161059905,-	p3@PVRL4
Hg19::chr1:161059935..161059942,-	p@chr1:161059935..161059942 -
Hg19::chr2:228382337..228382369,+	p@chr2:228382337..228382369 +
Hg19::chr5:80255192..80255201,+	p@chr5:80255192..80255201 +
Hg19::chr9:112261641..112261646,+	p@chr9:112261641..112261646 +

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:0042415	norepinephrine metabolic process	0.00350288472860002
GO:0042421	norepinephrine biosynthetic process	0.00350288472860002
GO:0048485	sympathetic nervous system development	0.00467044422881899
GO:0048483	autonomic nervous system development	0.00525417242194267
GO:0042423	catecholamine biosynthetic process	0.0140096828629117
GO:0042136	neurotransmitter biosynthetic process	0.0186779273270035
GO:0043627	response to estrogen stimulus	0.0198400389723906
GO:0006584	catecholamine metabolic process	0.0198400389723906
GO:0018958	phenol metabolic process	0.0198400389723906
GO:0001709	cell fate determination	0.0198400389723906
GO:0042133	neurotransmitter metabolic process	0.0198400389723906
GO:0042401	biogenic amine biosynthetic process	0.0198400389723906
GO:0048545	response to steroid hormone stimulus	0.019928932469712
GO:0042398	amino acid derivative biosynthetic process	0.0200707908551284
GO:0042446	hormone biosynthetic process	0.0200707908551284
GO:0042035	regulation of cytokine biosynthetic process	0.0248104870521948
GO:0042089	cytokine biosynthetic process	0.0248104870521948
GO:0042107	cytokine metabolic process	0.0248104870521948
GO:0045165	cell fate commitment	0.0248104870521948
GO:0006576	biogenic amine metabolic process	0.0248104870521948
GO:0009725	response to hormone stimulus	0.0248104870521948
GO:0001505	regulation of neurotransmitter levels	0.0248104870521948
GO:0042445	hormone metabolic process	0.0262372211764849
GO:0006575	amino acid derivative metabolic process	0.0262372211764849
GO:0001816	cytokine production	0.0316138775295708
GO:0009309	amine biosynthetic process	0.0320091784237637
GO:0050954	sensory perception of mechanical stimulus	0.032963518626922
GO:0007605	sensory perception of sound	0.032963518626922
GO:0044271	nitrogen compound biosynthetic process	0.0354356923500112
GO:0006725	aromatic compound metabolic process	0.0414706298862488
GO:0006417	regulation of translation	0.0414706298862488
GO:0031326	regulation of cellular biosynthetic process	0.0434401632898297
GO:0009889	regulation of biosynthetic process	0.0457994655493675
GO:0045893	positive regulation of transcription, DNA-dependent	0.0457994655493675

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
chorionic membrane mesenchymal stem cell	1.41e-46	3
germ line cell	2.32e-20	7
germ cell	2.32e-20	7
extraembryonic cell	3.48e-20	19
amnion mesenchymal stem cell	3.65e-13	5

Uber Anatomy

Ontology term	p-value	n
acellular anatomical structure	1.41e-46	3
egg chorion	1.41e-46	3
extraembryonic membrane	4.67e-39	14
membranous layer	4.67e-39	14
chorion	2.15e-35	7
extraembryonic structure	9.22e-23	24
amnion	1.13e-09	7
somatic layer of lateral plate mesoderm	1.42e-08	8
organ component layer	3.86e-08	66

Disease

Ontology term	p-value	n
islet cell tumor	1.04e-16	1
endocrine pancreas cancer	1.04e-16	1
pancreatic endocrine carcinoma	1.04e-16	1
germ cell and embryonal cancer	7.03e-07	22
germ cell cancer	7.03e-07	22

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)
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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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No analysis results for this cluster

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.