Coexpression cluster:C3944

Full id: C3944_Hepatocyte_kidney_xeroderma_epididymis_acute_diaphragm_colon

Phase1 CAGE Peaks

Hg19::chr1:226068355..226068367,-	p@chr1:226068355..226068367 -
Hg19::chr20:43030047..43030056,+	p7@HNF4A
Hg19::chr4:105828492..105828510,+	p1@ENST00000506148

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:0016439	tRNA-pseudouridine synthase activity	0.0256655213384284
GO:0009982	pseudouridine synthase activity	0.0256655213384284
GO:0016866	intramolecular transferase activity	0.0256655213384284
GO:0005496	steroid binding	0.0256655213384284
GO:0007596	blood coagulation	0.0256655213384284
GO:0050817	coagulation	0.0256655213384284
GO:0007599	hemostasis	0.0256655213384284
GO:0003707	steroid hormone receptor activity	0.0256655213384284
GO:0050878	regulation of body fluid levels	0.0256655213384284
GO:0042060	wound healing	0.0256655213384284
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0256655213384284
GO:0004879	ligand-dependent nuclear receptor activity	0.0258963263864359
GO:0045893	positive regulation of transcription, DNA-dependent	0.0348409097084477
GO:0003702	RNA polymerase II transcription factor activity	0.0366864623807842
GO:0045941	positive regulation of transcription	0.0366864623807842
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0366864623807842
GO:0016853	isomerase activity	0.0375153240384815
GO:0031325	positive regulation of cellular metabolic process	0.0409118433668062
GO:0009893	positive regulation of metabolic process	0.0409118433668062
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0409118433668062
GO:0009611	response to wounding	0.0409118433668062

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><br>

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Uber Anatomy

Ontology term	p-value	n
epididymis	1.21e-16	1
open tracheal system trachea	8.74e-09	2
abdomen element	3.52e-07	54
abdominal segment element	3.52e-07	54

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
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225909556731809

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.