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Coexpression cluster:C3016: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002294!1.11e-08!9;UBERON:0001173!1.11e-08!9;UBERON:0004912!1.11e-08!9;UBERON:0000489!5.61e-08!31;UBERON:0005177!9.62e-08!101;UBERON:0002394!9.67e-08!6;UBERON:0003928!9.67e-08!6;UBERON:0002113!1.77e-07!26;UBERON:0003918!1.77e-07!26;UBERON:0011143!1.77e-07!26;UBERON:0005095!1.77e-07!26;UBERON:0007687!1.77e-07!26;UBERON:0004810!2.97e-07!10;UBERON:0004211!3.92e-07!15;UBERON:0009773!3.92e-07!15;UBERON:0001231!3.92e-07!15;UBERON:0001285!3.92e-07!15;UBERON:0007684!3.92e-07!15;UBERON:0004208!3.92e-07!15;UBERON:0006853!8.55e-07!3;UBERON:0007685!8.55e-07!3;UBERON:0004134!8.55e-07!3
|ontology_enrichment_uberon=UBERON:0002294!1.11e-08!9;UBERON:0001173!1.11e-08!9;UBERON:0004912!1.11e-08!9;UBERON:0000489!5.61e-08!31;UBERON:0005177!9.62e-08!101;UBERON:0002394!9.67e-08!6;UBERON:0003928!9.67e-08!6;UBERON:0002113!1.77e-07!26;UBERON:0003918!1.77e-07!26;UBERON:0011143!1.77e-07!26;UBERON:0005095!1.77e-07!26;UBERON:0007687!1.77e-07!26;UBERON:0004810!2.97e-07!10;UBERON:0004211!3.92e-07!15;UBERON:0009773!3.92e-07!15;UBERON:0001231!3.92e-07!15;UBERON:0001285!3.92e-07!15;UBERON:0007684!3.92e-07!15;UBERON:0004208!3.92e-07!15;UBERON:0006853!8.55e-07!3;UBERON:0007685!8.55e-07!3;UBERON:0004134!8.55e-07!3
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}}
}}

Revision as of 15:52, 26 November 2012


Full id: C3016_papillotubular_mucinous_bile_signet_bronchioalveolar_tubular_clear



Phase1 CAGE Peaks

Hg19::chr10:4191811..4191817,-p@chr10:4191811..4191817
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Hg19::chr17:70713965..70713974,-p@chr17:70713965..70713974
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Hg19::chr22:46022320..46022366,-p@chr22:46022320..46022366
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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
biliary system1.11e-089
biliary tree1.11e-089
biliary bud1.11e-089
cavitated compound organ5.61e-0831
trunk region element9.62e-08101
bile duct9.67e-086
digestive system duct9.67e-086
kidney1.77e-0726
kidney mesenchyme1.77e-0726
upper urinary tract1.77e-0726
kidney rudiment1.77e-0726
kidney field1.77e-0726
nephron tubule epithelium2.97e-0710
nephron epithelium3.92e-0715
renal tubule3.92e-0715
nephron tubule3.92e-0715
nephron3.92e-0715
uriniferous tubule3.92e-0715
nephrogenic mesenchyme3.92e-0715
renal cortex tubule8.55e-073
region of nephron tubule8.55e-073
proximal tubule8.55e-073
Disease
Ontology termp-valuen
carcinoma5.11e-36106
cell type cancer8.45e-25143
adenocarcinoma9.95e-2425
squamous cell carcinoma9.20e-1914
cancer1.20e-16235
disease of cellular proliferation3.88e-16239
signet ring cell adenocarcinoma1.68e-102
tubular adenocarcinoma1.76e-102


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.