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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous
|full_id=C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous
|id=C1262
|id=C1262

Revision as of 13:46, 12 September 2012


Full id: C1262_renal_clear_Renal_papillotubular_embryonic_mucinous_serous



Phase1 CAGE Peaks

Hg19::chr22:30653345..30653353,-p@chr22:30653345..30653353
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Hg19::chr22:30653384..30653392,-p@chr22:30653384..30653392
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Hg19::chr22:30653399..30653414,-p@chr22:30653399..30653414
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Hg19::chr22:30653425..30653444,-p@chr22:30653425..30653444
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Hg19::chr22:30653669..30653690,-p@chr22:30653669..30653690
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Hg19::chr22:30653699..30653718,-p@chr22:30653699..30653718
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Hg19::chr22:30653761..30653772,-p@chr22:30653761..30653772
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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

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

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>

Uber Anatomy
Ontology termp-valuen
duct3.31e-1326
kidney6.37e-1327
kidney mesenchyme6.37e-1327
kidney rudiment6.37e-1327
kidney field6.37e-1327
nephron epithelium1.14e-1116
nephron1.14e-1116
uriniferous tubule1.14e-1116
metanephric mesenchyme1.14e-1116
nephrogenic mesenchyme1.14e-1116
cavitated compound organ4.18e-1132
trunk region element4.66e-11107
organ7.81e-11511
excretory tube1.11e-1017
mesonephric epithelium1.11e-1017
mesonephric tubule1.11e-1017
nephric duct1.11e-1017
kidney epithelium1.11e-1017
renal duct1.11e-1017
mesonephric duct1.11e-1017
pronephric duct1.11e-1017
renal tubule2.03e-1012
nephron tubule2.03e-1012
nephron tubule epithelium2.03e-1012
mesoderm2.53e-10448
mesoderm-derived structure2.53e-10448
presumptive mesoderm2.53e-10448
abdomen element3.36e-1055
abdominal segment element3.36e-1055
urinary system structure5.47e-1044
mesonephros8.31e-1018
pronephros8.31e-1018
nephrogenic cord8.31e-1018
pronephric mesoderm8.31e-1018
rostral part of nephrogenic cord8.31e-1018
presumptive pronephric mesoderm8.31e-1018
renal system1.43e-0945
body cavity precursor3.37e-0963
cortex of kidney1.05e-0813
renal parenchyma1.05e-0813
immaterial anatomical entity1.26e-08126
parenchyma1.74e-0817
urogenital ridge2.43e-0820
abdominal segment of trunk3.17e-0861
abdomen3.17e-0861
cortex8.30e-0816
intraembryonic coelom1.02e-0721
larynx2.09e-079
biliary system2.16e-077
biliary tree2.16e-077
biliary bud2.16e-077
embryo2.38e-07612
anatomical cavity2.80e-0770
anatomical space2.90e-07104
intermediate mesoderm3.05e-0737
subdivision of digestive tract4.61e-07129
endodermal part of digestive tract4.61e-07129
small intestine6.03e-0714
germ layer7.63e-07604
embryonic tissue7.63e-07604
presumptive structure7.63e-07604
epiblast (generic)7.63e-07604
embryonic structure9.23e-07605
developing anatomical structure9.23e-07605
Disease
Ontology termp-valuen
carcinoma8.55e-22106
cell type cancer1.28e-19143
cancer3.13e-12235
disease of cellular proliferation2.00e-11239
adenocarcinoma3.94e-0925


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

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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POLR2A#543072.147453176558070.004747636447610280.0223541951648695
TFAP2C#7022710.80922860986025.79365976833206e-083.61244198534228e-06



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

This analysis result is provided for C0 - C305 clusters.

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