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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular
|full_id=C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular
|id=C3446
|id=C3446

Revision as of 16:22, 12 September 2012


Full id: C3446_Hepatocyte_bronchial_gall_signet_Prostate_smallcell_hepatocellular



Phase1 CAGE Peaks

Hg19::chr14:65406261..65406292,-p@chr14:65406261..65406292
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Hg19::chr14:65406411..65406422,-p@chr14:65406411..65406422
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Hg19::chr14:65406492..65406508,-p@chr14:65406492..65406508
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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
endoderm-derived structure2.90e-37169
endoderm2.90e-37169
presumptive endoderm2.90e-37169
digestive system2.62e-32155
digestive tract2.62e-32155
primitive gut2.62e-32155
subdivision of digestive tract9.10e-30129
endodermal part of digestive tract9.10e-30129
mixed endoderm/mesoderm-derived structure6.56e-22130
foregut8.73e-1898
respiratory system2.47e-1772
endo-epithelium1.18e-1682
immaterial anatomical entity3.85e-15126
orifice3.91e-1435
oral opening6.74e-1221
gut epithelium1.23e-1054
respiratory tract8.81e-1053
epithelium of foregut-midgut junction9.74e-1025
anatomical boundary9.74e-1025
hepatobiliary system9.74e-1025
foregut-midgut junction9.74e-1025
septum transversum9.74e-1025
trunk region element1.01e-09107
gastrointestinal system1.58e-0935
anatomical space1.77e-09104
exocrine gland2.27e-0931
exocrine system2.27e-0931
digestive tract diverticulum5.57e-0923
thoracic cavity element7.19e-0934
thoracic cavity7.19e-0934
thoracic segment organ1.65e-0835
intestine2.44e-0827
mesenchyme3.43e-08238
entire embryonic mesenchyme3.43e-08238
mouth3.88e-0828
stomodeum3.88e-0828
hepatic diverticulum8.31e-0822
liver primordium8.31e-0822
sac1.26e-0726
liver1.55e-0719
digestive gland1.55e-0719
liver bud1.55e-0719
tracheobronchial tree1.59e-0714
lower respiratory tract1.59e-0714
multi-tissue structure3.79e-07347
lower respiratory tract epithelium8.27e-073
epithelium of bronchus8.27e-073
Disease
Ontology termp-valuen
carcinoma9.22e-11106
squamous cell carcinoma1.15e-0714
cell type cancer5.71e-07143


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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