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|ontology_enrichment_disease=DOID:120!2.27e-10!27;DOID:193!3.16e-09!29;DOID:299!9.31e-09!25
|ontology_enrichment_disease=DOID:120!2.27e-10!27;DOID:193!3.16e-09!29;DOID:299!9.31e-09!25
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}}
}}

Revision as of 17:20, 8 August 2012


Full id: C1493_clear_thyroid_endometrioid_serous_throat_anaplastic_renal



Phase1 CAGE Peaks

Hg19::chr2:113982484..113982512,-p@chr2:113982484..113982512
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Hg19::chr2:113982581..113982590,-p@chr2:113982581..113982590
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Hg19::chr2:113982635..113982648,-p8@PAX8
Hg19::chr2:113994209..113994222,-p11@PAX8
Hg19::chr2:114002042..114002053,-p@chr2:114002042..114002053
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Hg19::chr2:114002106..114002117,-p@chr2:114002106..114002117
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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>

Cell Type
Ontology termp-valuen
kidney cell7.10e-1118
kidney epithelial cell7.10e-1118
kidney tubule cell5.02e-0912
nephron tubule epithelial cell5.02e-0912
epithelial cell of nephron6.41e-0916
oligodendrocyte7.21e-077
macroglial cell7.21e-077
astrocyte7.21e-077
oligodendrocyte precursor cell7.21e-077
Uber Anatomy
Ontology termp-valuen
cavitated compound organ2.12e-1532
duct4.81e-1326
kidney3.84e-1227
kidney mesenchyme3.84e-1227
kidney rudiment3.84e-1227
kidney field3.84e-1227
renal system3.69e-1145
body cavity precursor5.10e-1163
mesonephros7.10e-1118
pronephros7.10e-1118
nephrogenic cord7.10e-1118
pronephric mesoderm7.10e-1118
rostral part of nephrogenic cord7.10e-1118
presumptive pronephric mesoderm7.10e-1118
urinary system structure1.82e-1044
anatomical cavity2.84e-1070
excretory tube7.07e-1017
mesonephric epithelium7.07e-1017
mesonephric tubule7.07e-1017
nephric duct7.07e-1017
kidney epithelium7.07e-1017
renal duct7.07e-1017
mesonephric duct7.07e-1017
pronephric duct7.07e-1017
intraembryonic coelom1.33e-0921
urogenital ridge2.70e-0920
compound organ4.67e-0969
renal tubule5.02e-0912
nephron tubule5.02e-0912
nephron tubule epithelium5.02e-0912
nephron epithelium6.41e-0916
nephron6.41e-0916
uriniferous tubule6.41e-0916
metanephric mesenchyme6.41e-0916
nephrogenic mesenchyme6.41e-0916
intermediate mesoderm9.53e-0937
reproductive organ2.13e-0748
reproductive structure5.36e-0759
reproductive system5.36e-0759
Disease
Ontology termp-valuen
female reproductive organ cancer2.27e-1027
reproductive organ cancer3.16e-0929
adenocarcinoma9.31e-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)

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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

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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