Coexpression cluster:C889

Full id: C889_mesothelioma_mesodermal_lung_placenta_umbilical_Urothelial_Mallassezderived

Phase1 CAGE Peaks

Hg19::chr12:106477805..106477824,-	p13@NUAK1
Hg19::chr12:80175910..80175928,-	p31@PPP1R12A
Hg19::chr17:26890530..26890545,-	p@chr17:26890530..26890545 -
Hg19::chr17:26890583..26890593,-	p@chr17:26890583..26890593 -
Hg19::chr17:67586124..67586131,+	p1@uc002jil.2
Hg19::chr3:129023260..129023267,+	p3@AF035296
Hg19::chr4:23022304..23022336,+	p@chr4:23022304..23022336 +
Hg19::chr8:141728444..141728461,-	p23@PTK2
Hg19::chr8:141728472..141728496,-	p19@PTK2

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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p.value	FDR	nGenes	nPathway	Name
0.000145853209864357	0.0264257502200088	2	200	Focal adhesion (KEGG):04510
0.000166987363159613	0.0264257502200088	2	214	Regulation of actin cytoskeleton (KEGG):04810
0.000128870835041632	0.0264257502200088	2	188	Focal Adhesion (Wikipathways):WP306
7.66167144514812e-05	0.0264257502200088	2	145	Regulation of Actin Cytoskeleton (Wikipathways):WP51

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:0007172	signal complex assembly	0.0300359574741371
GO:0042169	SH2 domain binding	0.0300359574741371
GO:0005925	focal adhesion	0.0300359574741371
GO:0005924	cell-substrate adherens junction	0.0300359574741371
GO:0004672	protein kinase activity	0.0300359574741371
GO:0006937	regulation of muscle contraction	0.0300359574741371
GO:0006468	protein amino acid phosphorylation	0.0300359574741371
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0300359574741371
GO:0030055	cell-matrix junction	0.0300359574741371
GO:0005912	adherens junction	0.0300359574741371
GO:0016310	phosphorylation	0.0300359574741371
GO:0016773	phosphotransferase activity, alcohol group as acceptor	0.0300359574741371
GO:0005856	cytoskeleton	0.0300359574741371
GO:0043623	cellular protein complex assembly	0.030700721916763
GO:0016301	kinase activity	0.030700721916763
GO:0006793	phosphorus metabolic process	0.030700721916763
GO:0006796	phosphate metabolic process	0.030700721916763
GO:0016323	basolateral plasma membrane	0.030700721916763
GO:0007229	integrin-mediated signaling pathway	0.030700721916763
GO:0016772	transferase activity, transferring phosphorus-containing groups	0.0369879296170742
GO:0019904	protein domain specific binding	0.0409697638742895
GO:0043687	post-translational protein modification	0.0434369027088801
GO:0003012	muscle system process	0.0465227350691899
GO:0006936	muscle contraction	0.0465227350691899
GO:0006464	protein modification process	0.0492255124386033
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0492255124386033
GO:0005515	protein binding	0.0492255124386033
GO:0005524	ATP binding	0.0492255124386033
GO:0043412	biopolymer modification	0.0492255124386033
GO:0032559	adenyl ribonucleotide binding	0.0492255124386033
GO:0043232	intracellular non-membrane-bound organelle	0.0492255124386033
GO:0043228	non-membrane-bound organelle	0.0492255124386033
GO:0030554	adenyl nucleotide binding	0.0492255124386033

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
mesothelial cell	2.15e-20	19
cortical cell of adrenal gland	3.71e-09	2

Uber Anatomy

Ontology term	p-value	n
urinary bladder	6.94e-09	2
lower urinary tract	6.94e-09	2

Disease

Ontology term	p-value	n
papillary adenocarcinoma	1.04e-16	1

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.