Coexpression cluster:C4540

Full id: C4540_serous_renal_Hepatocyte_signet_gall_liver_kidney

Phase1 CAGE Peaks

Hg19::chr6:107235234..107235237,-	p3@LOC100422737
Hg19::chr6:107235249..107235267,-	p1@LOC100422737
Hg19::chr6:107235287..107235303,-	p2@LOC100422737

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
metabolising cell	6.97e-16	12
endopolyploid cell	6.97e-16	12
parenchymal cell	6.97e-16	12
polyploid cell	6.97e-16	12
hepatocyte	6.97e-16	12
kidney cell	2.22e-07	18
kidney epithelial cell	2.22e-07	18
endodermal cell	3.82e-07	59

Uber Anatomy

Ontology term	p-value	n
abdomen element	2.29e-24	55
abdominal segment element	2.29e-24	55
abdominal segment of trunk	1.78e-21	61
abdomen	1.78e-21	61
epithelium of foregut-midgut junction	1.33e-17	25
anatomical boundary	1.33e-17	25
hepatobiliary system	1.33e-17	25
foregut-midgut junction	1.33e-17	25
septum transversum	1.33e-17	25
hepatic diverticulum	1.18e-16	22
liver primordium	1.18e-16	22
liver	5.90e-16	19
digestive gland	5.90e-16	19
liver bud	5.90e-16	19
digestive tract diverticulum	7.71e-16	23
trunk region element	1.49e-15	107
epithelial sac	2.08e-14	25
sac	8.94e-14	26
immune organ	1.21e-13	26
gut epithelium	2.56e-11	54
immaterial anatomical entity	6.25e-11	126
subdivision of trunk	1.52e-10	113
cavitated compound organ	2.02e-10	32
kidney	2.21e-10	27
kidney mesenchyme	2.21e-10	27
kidney rudiment	2.21e-10	27
kidney field	2.21e-10	27
urinary system structure	3.53e-10	44
renal system	6.75e-10	45
exocrine gland	4.07e-09	31
exocrine system	4.07e-09	31
endocrine system	1.14e-08	45
endocrine gland	6.93e-08	35
endo-epithelium	1.61e-07	82
mixed endoderm/mesoderm-derived structure	2.44e-07	130
subdivision of digestive tract	2.78e-07	129
endodermal part of digestive tract	2.78e-07	129
gland	3.48e-07	59
trunk	6.82e-07	216

Disease

Ontology term	p-value	n
adenocarcinoma	6.84e-09	25
clear cell adenocarcinoma	8.35e-09	2
carcinoma	7.78e-07	106

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.