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Coexpression cluster:C2479: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.07e-31!106;DOID:0050687!5.74e-27!143;DOID:162!1.43e-23!235;DOID:14566!1.07e-22!239;DOID:1749!1.56e-16!14;DOID:299!4.49e-13!25;DOID:1036!3.95e-09!8;DOID:7!6.23e-08!39
|ontology_enrichment_disease=DOID:305!3.07e-31!106;DOID:0050687!5.74e-27!143;DOID:162!1.43e-23!235;DOID:14566!1.07e-22!239;DOID:1749!1.56e-16!14;DOID:299!4.49e-13!25;DOID:1036!3.95e-09!8;DOID:7!6.23e-08!39
|ontology_enrichment_uberon=UBERON:0002294!1.67e-10!7;UBERON:0001173!1.67e-10!7;UBERON:0004912!1.67e-10!7;UBERON:0000344!5.41e-08!12;UBERON:0000476!9.56e-08!3;UBERON:0000920!9.56e-08!3
|ontology_enrichment_uberon=UBERON:0002294!1.67e-10!7;UBERON:0001173!1.67e-10!7;UBERON:0004912!1.67e-10!7;UBERON:0000344!5.41e-08!12;UBERON:0000476!9.56e-08!3;UBERON:0000920!9.56e-08!3
|tf_chipseq_enrich=TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279469650385918
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}}
}}

Revision as of 11:40, 5 September 2012


Full id: C2479_Wilms_clear_rectal_chorionic_epidermoid_acantholytic_liposarcoma



Phase1 CAGE Peaks

Hg19::chr19:15939963..15939981,+p3@UCA1
Hg19::chr19:15940032..15940045,+p5@UCA1
Hg19::chr19:15945585..15945607,-p@chr19:15945585..15945607
-
Hg19::chr19:15945775..15945784,+p@chr19:15945775..15945784
+


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 cell6.61e-18254
endodermal cell2.69e-0859
chorionic membrane mesenchymal stem cell9.56e-083
epithelial cell of alimentary canal1.05e-0721
endo-epithelial cell4.23e-0743
Uber Anatomy
Ontology termp-valuen
biliary system1.67e-107
biliary tree1.67e-107
biliary bud1.67e-107
mucosa5.41e-0812
acellular anatomical structure9.56e-083
egg chorion9.56e-083
Disease
Ontology termp-valuen
carcinoma3.07e-31106
cell type cancer5.74e-27143
cancer1.43e-23235
disease of cellular proliferation1.07e-22239
squamous cell carcinoma1.56e-1614
adenocarcinoma4.49e-1325
chronic leukemia3.95e-098
disease of anatomical entity6.23e-0839


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
TAL1#6886214.93430833872010.006428077577888070.0279469650385918



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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