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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3652_Bronchial_meningioma_papillary_Prostate_mesenchymal_Tracheal_Urothelial
|full_id=C3652_Bronchial_meningioma_papillary_Prostate_mesenchymal_Tracheal_Urothelial
|id=C3652
|id=C3652

Revision as of 16:36, 12 September 2012


Full id: C3652_Bronchial_meningioma_papillary_Prostate_mesenchymal_Tracheal_Urothelial



Phase1 CAGE Peaks

Hg19::chr17:48141446..48141483,+p@chr17:48141446..48141483
+
Hg19::chr17:48145468..48145508,+p@chr17:48145468..48145508
+
Hg19::chr17:48149430..48149463,+p5@ITGA3


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
multi-tissue structure1.86e-14347
mesenchyme4.39e-13238
entire embryonic mesenchyme4.39e-13238
trunk mesenchyme4.71e-12143
organism subdivision3.52e-11365
trunk1.01e-10216
cell layer4.67e-10312
duct7.52e-1026
epithelium7.70e-10309
nephron epithelium1.32e-0916
nephron1.32e-0916
uriniferous tubule1.32e-0916
metanephric mesenchyme1.32e-0916
nephrogenic mesenchyme1.32e-0916
urogenital ridge1.86e-0920
excretory tube4.16e-0917
mesonephric epithelium4.16e-0917
mesonephric tubule4.16e-0917
nephric duct4.16e-0917
kidney epithelium4.16e-0917
renal duct4.16e-0917
mesonephric duct4.16e-0917
pronephric duct4.16e-0917
mesonephros5.87e-0918
pronephros5.87e-0918
nephrogenic cord5.87e-0918
pronephric mesoderm5.87e-0918
rostral part of nephrogenic cord5.87e-0918
presumptive pronephric mesoderm5.87e-0918
multilaminar epithelium8.51e-0982
epithelial tube6.65e-08118
cortex of kidney7.50e-0813
renal parenchyma7.50e-0813
parenchyma8.35e-0817
renal tubule1.04e-0712
nephron tubule1.04e-0712
nephron tubule epithelium1.04e-0712
somite1.27e-0783
paraxial mesoderm1.27e-0783
presomitic mesoderm1.27e-0783
presumptive segmental plate1.27e-0783
trunk paraxial mesoderm1.27e-0783
presumptive paraxial mesoderm1.27e-0783
anatomical system1.44e-07625
multi-cellular organism1.64e-07659
urinary system structure1.93e-0744
intermediate mesoderm2.01e-0737
anatomical group2.17e-07626
primordium2.49e-07168
intraembryonic coelom2.58e-0721
anatomical space3.17e-07104
renal system6.23e-0745
ectodermal placode7.25e-0729
dermomyotome7.44e-0770
Disease
Ontology termp-valuen
reproductive organ cancer4.45e-0829
female reproductive organ cancer5.67e-0827


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

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

This analysis result is provided for C0 - C305 clusters.

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