Coexpression cluster:C1357

Full id: C1357_Mesenchymal_Alveolar_Renal_Placental_acantholytic_Tracheal_Bronchial

Phase1 CAGE Peaks

Hg19::chr12:132628963..132629027,+	p1@NOC4L
Hg19::chr12:53895052..53895143,+	p1@TARBP2
Hg19::chr16:2022036..2022112,+	p1@TBL3
Hg19::chr16:88772866..88772947,+	p1@CTU2
Hg19::chr19:59055814..59055835,+	p1@TRIM28
Hg19::chr19:984313..984357,+	p1@WDR18

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:0007199	G-protein signaling, coupled to cGMP nucleotide second messenger	0.011538404895764
GO:0019934	cGMP-mediated signaling	0.011538404895764
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0172999664284364
GO:0030515	snoRNA binding	0.0172999664284364
GO:0005634	nucleus	0.0172999664284364
GO:0043193	positive regulation of gene-specific transcription	0.0172999664284364
GO:0001837	epithelial to mesenchymal transition	0.0172999664284364
GO:0032583	regulation of gene-specific transcription	0.0172999664284364
GO:0005732	small nucleolar ribonucleoprotein complex	0.0192196385985799
GO:0006366	transcription from RNA polymerase II promoter	0.0203185721744452
GO:0048762	mesenchymal cell differentiation	0.0230544017185297
GO:0014031	mesenchymal cell development	0.0230544017185297
GO:0043231	intracellular membrane-bound organelle	0.0295162839166376
GO:0043227	membrane-bound organelle	0.0295162839166376
GO:0003723	RNA binding	0.0295162839166376
GO:0044452	nucleolar part	0.0295162839166376
GO:0003725	double-stranded RNA binding	0.0358917455404646

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

Uber Anatomy

Ontology term	p-value	n

Disease

Ontology term	p-value	n

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.