Coexpression cluster:C4518

Full id: C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal

Phase1 CAGE Peaks

Hg19::chr5:73109300..73109311,+	p5@RGNEF
Hg19::chr5:73109313..73109326,+	p4@RGNEF
Hg19::chr5:73109339..73109409,+	p2@RGNEF

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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No GOStat results

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
kidney cell	2.78e-08	18
kidney epithelial cell	2.78e-08	18
kidney tubule cell	2.40e-07	12
nephron tubule epithelial cell	2.40e-07	12
endo-epithelial cell	7.73e-07	43
epithelial cell of nephron	9.34e-07	16

Uber Anatomy

Ontology term	p-value	n
reproductive organ	5.60e-13	48
reproductive structure	1.40e-12	59
reproductive system	1.40e-12	59
female organism	7.41e-12	41
cavitated compound organ	1.33e-11	32
female reproductive organ	7.66e-11	37
female reproductive system	7.66e-11	37
renal system	1.12e-10	45
kidney	1.93e-10	27
kidney mesenchyme	1.93e-10	27
kidney rudiment	1.93e-10	27
kidney field	1.93e-10	27
urinary system structure	3.54e-10	44
urogenital ridge	2.36e-09	20
organism subdivision	2.74e-09	365
body cavity precursor	1.15e-08	63
duct	2.52e-08	26
mesonephros	4.73e-08	18
pronephros	4.73e-08	18
nephrogenic cord	4.73e-08	18
pronephric mesoderm	4.73e-08	18
rostral part of nephrogenic cord	4.73e-08	18
presumptive pronephric mesoderm	4.73e-08	18
anatomical space	5.67e-08	104
anatomical cavity	9.68e-08	70
female gonad	1.41e-07	13
embryo	1.42e-07	612
gonad	1.90e-07	21
indifferent external genitalia	1.90e-07	21
indifferent gonad	1.90e-07	21
gonad primordium	1.90e-07	21
excretory tube	1.99e-07	17
mesonephric epithelium	1.99e-07	17
mesonephric tubule	1.99e-07	17
nephric duct	1.99e-07	17
kidney epithelium	1.99e-07	17
renal duct	1.99e-07	17
mesonephric duct	1.99e-07	17
pronephric duct	1.99e-07	17
multi-tissue structure	2.11e-07	347
renal tubule	2.40e-07	12
nephron tubule	2.40e-07	12
nephron tubule epithelium	2.40e-07	12
intermediate mesoderm	2.98e-07	37
embryonic structure	3.79e-07	605
developing anatomical structure	3.79e-07	605
internal genitalia	4.72e-07	25
multi-cellular organism	6.04e-07	659
germ layer	6.94e-07	604
embryonic tissue	6.94e-07	604
presumptive structure	6.94e-07	604
epiblast (generic)	6.94e-07	604
trunk	7.43e-07	216
external genitalia	7.72e-07	22
nephron epithelium	9.34e-07	16
nephron	9.34e-07	16
uriniferous tubule	9.34e-07	16
metanephric mesenchyme	9.34e-07	16
nephrogenic mesenchyme	9.34e-07	16

Disease

Ontology term	p-value	n
female reproductive organ cancer	3.24e-12	27
reproductive organ cancer	1.03e-10	29
ovarian cancer	4.57e-10	14

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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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.