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Coexpression cluster:C4181: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003343!7.78e-10!4;UBERON:0004785!7.78e-10!4;UBERON:0000344!1.14e-09!20;UBERON:0000166!1.49e-08!22;UBERON:0003729!3.67e-08!13;UBERON:0000161!4.96e-08!36;UBERON:0001949!5.04e-08!3;UBERON:0003350!3.06e-07!8;UBERON:0005631!3.40e-07!14;UBERON:0000158!3.40e-07!14;UBERON:0004923!6.56e-07!66;UBERON:0004175!8.13e-07!25;UBERON:0001911!8.55e-07!4;UBERON:0005333!8.55e-07!4;UBERON:0008425!8.55e-07!4;UBERON:0005311!8.55e-07!4
|ontology_enrichment_uberon=UBERON:0003343!7.78e-10!4;UBERON:0004785!7.78e-10!4;UBERON:0000344!1.14e-09!20;UBERON:0000166!1.49e-08!22;UBERON:0003729!3.67e-08!13;UBERON:0000161!4.96e-08!36;UBERON:0001949!5.04e-08!3;UBERON:0003350!3.06e-07!8;UBERON:0005631!3.40e-07!14;UBERON:0000158!3.40e-07!14;UBERON:0004923!6.56e-07!66;UBERON:0004175!8.13e-07!25;UBERON:0001911!8.55e-07!4;UBERON:0005333!8.55e-07!4;UBERON:0008425!8.55e-07!4;UBERON:0005311!8.55e-07!4
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}}
}}

Revision as of 16:36, 26 November 2012


Full id: C4181_breast_ductal_bile_Mammary_Prostate_oral_malignant



Phase1 CAGE Peaks

Hg19::chr2:216003325..216003359,-p1@ABCA12
Hg19::chr2:216003367..216003380,-p3@ABCA12
Hg19::chr2:216003387..216003397,-p4@ABCA12


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
epithelial cell5.30e-20253
endo-epithelial cell4.03e-1942
endodermal cell2.86e-1558
epithelial cell of alimentary canal7.61e-1220
gingival epithelial cell5.04e-083
mammary gland epithelial cell8.55e-074
Uber Anatomy
Ontology termp-valuen
mucosa of oral region7.78e-104
respiratory system mucosa7.78e-104
mucosa1.14e-0920
oral opening1.49e-0822
mouth mucosa3.67e-0813
orifice4.96e-0836
gingival epithelium5.04e-083
epithelium of mucosa3.06e-078
extraembryonic membrane3.40e-0714
membranous layer3.40e-0714
organ component layer6.56e-0766
internal genitalia8.13e-0725
mammary gland8.55e-074
mammary bud8.55e-074
mammary ridge8.55e-074
mammary placode8.55e-074
Disease
Ontology termp-valuen
squamous cell carcinoma7.54e-1814
carcinoma8.27e-15106
cell type cancer3.62e-12143
thoracic cancer8.68e-114
breast cancer8.68e-114


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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