Coexpression cluster:C2387

Full id: C2387_kidney_renal_serous_smallcell_clear_mesothelioma_HES3GFP

Phase1 CAGE Peaks

Hg19::chr16:71879001..71879011,+	p@chr16:71879001..71879011 +
Hg19::chr1:18807489..18807496,+	p3@KLHDC7A
Hg19::chr1:18807498..18807518,+	p1@KLHDC7A
Hg19::chr8:107593246..107593259,+	p14@OXR1

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:0016998	cell wall catabolic process	0.00339985870717061
GO:0007047	cell wall organization and biogenesis	0.00339985870717061
GO:0010382	cell wall metabolic process	0.00339985870717061
GO:0045229	external encapsulating structure organization and biogenesis	0.00339985870717061
GO:0006979	response to oxidative stress	0.0148357470858354

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	2.08e-10	254
kidney tubule cell	5.77e-08	12
nephron tubule epithelial cell	5.77e-08	12
endodermal cell	6.51e-08	59
embryonic stem cell	1.39e-07	5
kidney cell	3.70e-07	18
kidney epithelial cell	3.70e-07	18

Uber Anatomy

Ontology term	p-value	n
trunk region element	6.30e-12	107
abdomen element	4.09e-11	55
abdominal segment element	4.09e-11	55
immaterial anatomical entity	1.81e-10	126
subdivision of trunk	6.67e-10	113
abdominal segment of trunk	6.95e-10	61
abdomen	6.95e-10	61
duct	2.48e-09	26
kidney	2.73e-09	27
kidney mesenchyme	2.73e-09	27
kidney rudiment	2.73e-09	27
kidney field	2.73e-09	27
cavitated compound organ	3.57e-09	32
subdivision of digestive tract	2.90e-08	129
endodermal part of digestive tract	2.90e-08	129
renal tubule	5.77e-08	12
nephron tubule	5.77e-08	12
nephron tubule epithelium	5.77e-08	12
renal system	1.86e-07	45
digestive system	3.34e-07	155
digestive tract	3.34e-07	155
primitive gut	3.34e-07	155
epithelial sac	3.84e-07	25
anatomical space	4.04e-07	104
multi-tissue structure	5.68e-07	347
mesonephros	6.17e-07	18
pronephros	6.17e-07	18
nephrogenic cord	6.17e-07	18
pronephric mesoderm	6.17e-07	18
rostral part of nephrogenic cord	6.17e-07	18
presumptive pronephric mesoderm	6.17e-07	18
urinary system structure	6.83e-07	44

Disease

Ontology term	p-value	n
carcinoma	3.06e-14	106
cell type cancer	1.28e-10	143
adenocarcinoma	2.94e-10	25

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
BCL11A#53335	2	14.1847275518035	0.00710832858529874	0.0296196428790303
CTBP2#1488	2	31.3585001696641	0.00149267688204723	0.0095394493259167
ESR1#2099	2	15.3843016480772	0.00606557262969351	0.0268367862686956
HNF4A#3172	2	11.5661451814768	0.0105758568176249	0.0390666682055647
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.0284846527842871

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.