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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal
|full_id=C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal
|id=C4518
|id=C4518

Revision as of 17:36, 12 September 2012


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

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>

Cell Type
Ontology termp-valuen
kidney cell2.78e-0818
kidney epithelial cell2.78e-0818
kidney tubule cell2.40e-0712
nephron tubule epithelial cell2.40e-0712
endo-epithelial cell7.73e-0743
epithelial cell of nephron9.34e-0716
Uber Anatomy
Ontology termp-valuen
reproductive organ5.60e-1348
reproductive structure1.40e-1259
reproductive system1.40e-1259
female organism7.41e-1241
cavitated compound organ1.33e-1132
female reproductive organ7.66e-1137
female reproductive system7.66e-1137
renal system1.12e-1045
kidney1.93e-1027
kidney mesenchyme1.93e-1027
kidney rudiment1.93e-1027
kidney field1.93e-1027
urinary system structure3.54e-1044
urogenital ridge2.36e-0920
organism subdivision2.74e-09365
body cavity precursor1.15e-0863
duct2.52e-0826
mesonephros4.73e-0818
pronephros4.73e-0818
nephrogenic cord4.73e-0818
pronephric mesoderm4.73e-0818
rostral part of nephrogenic cord4.73e-0818
presumptive pronephric mesoderm4.73e-0818
anatomical space5.67e-08104
anatomical cavity9.68e-0870
female gonad1.41e-0713
embryo1.42e-07612
gonad1.90e-0721
indifferent external genitalia1.90e-0721
indifferent gonad1.90e-0721
gonad primordium1.90e-0721
excretory tube1.99e-0717
mesonephric epithelium1.99e-0717
mesonephric tubule1.99e-0717
nephric duct1.99e-0717
kidney epithelium1.99e-0717
renal duct1.99e-0717
mesonephric duct1.99e-0717
pronephric duct1.99e-0717
multi-tissue structure2.11e-07347
renal tubule2.40e-0712
nephron tubule2.40e-0712
nephron tubule epithelium2.40e-0712
intermediate mesoderm2.98e-0737
embryonic structure3.79e-07605
developing anatomical structure3.79e-07605
internal genitalia4.72e-0725
multi-cellular organism6.04e-07659
germ layer6.94e-07604
embryonic tissue6.94e-07604
presumptive structure6.94e-07604
epiblast (generic)6.94e-07604
trunk7.43e-07216
external genitalia7.72e-0722
nephron epithelium9.34e-0716
nephron9.34e-0716
uriniferous tubule9.34e-0716
metanephric mesenchyme9.34e-0716
nephrogenic mesenchyme9.34e-0716
Disease
Ontology termp-valuen
female reproductive organ cancer3.24e-1227
reproductive organ cancer1.03e-1029
ovarian cancer4.57e-1014


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
USF1#739136.361499277207960.00388404057290560.0190990777999759



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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