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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma
|full_id=C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma
|id=C2079
|id=C2079

Revision as of 14:45, 12 September 2012


Full id: C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr10:91316455..91316462,-p4@SLC16A12
Hg19::chr3:114464766..114464816,-p@chr3:114464766..114464816
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Hg19::chr3:114464819..114464840,-p@chr3:114464819..114464840
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Hg19::chr3:114464843..114464849,-p@chr3:114464843..114464849
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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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure3.45e-15347
adult organism1.93e-12115
mesenchyme2.53e-12238
entire embryonic mesenchyme2.53e-12238
organism subdivision9.33e-12365
endoderm-derived structure6.35e-10169
endoderm6.35e-10169
presumptive endoderm6.35e-10169
trunk6.66e-10216
abdomen element1.11e-0955
abdominal segment element1.11e-0955
abdominal segment of trunk1.80e-0961
abdomen1.80e-0961
cell layer1.97e-09312
organ2.10e-09511
trunk mesenchyme3.77e-09143
sac3.83e-0926
anatomical cluster6.06e-09286
mixed endoderm/mesoderm-derived structure7.52e-09130
epithelium7.54e-09309
digestive system8.12e-09155
digestive tract8.12e-09155
primitive gut8.12e-09155
immaterial anatomical entity1.22e-08126
epithelial sac1.40e-0825
duct1.46e-0826
subdivision of digestive tract2.03e-08129
endodermal part of digestive tract2.03e-08129
renal system2.09e-0845
urinary system structure4.90e-0844
multi-cellular organism4.93e-08659
epithelium of foregut-midgut junction9.46e-0825
anatomical boundary9.46e-0825
hepatobiliary system9.46e-0825
foregut-midgut junction9.46e-0825
septum transversum9.46e-0825
trunk region element1.15e-07107
gut epithelium1.32e-0754
digestive tract diverticulum2.65e-0723
subdivision of trunk3.59e-07113
primordium5.70e-07168
anatomical conduit7.95e-07241
hepatic diverticulum9.18e-0722
liver primordium9.18e-0722
anatomical system9.96e-07625


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
CEBPB#105135.978360719368610.007153832484726970.0297144094365415
FOSL2#2355312.69765045342130.000787568572975710.00616542044771832
NR3C1#2908414.9730233311731.98868032687801e-050.000441811922269331
USF1#739134.771124457905970.01370465887188020.048266704927507



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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