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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4653_large_lung_glioblastoma_hepatoma_mesothelioma_endometrial_pleomorphic
|full_id=C4653_large_lung_glioblastoma_hepatoma_mesothelioma_endometrial_pleomorphic
|id=C4653
|id=C4653

Revision as of 17:45, 12 September 2012


Full id: C4653_large_lung_glioblastoma_hepatoma_mesothelioma_endometrial_pleomorphic



Phase1 CAGE Peaks

Hg19::chr7:134212296..134212311,+p2@AKR1B10
Hg19::chr7:134212312..134212329,+p1@AKR1B10
Hg19::chr7:134212586..134212595,+p6@AKR1B10


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 cell5.91e-19254
endodermal cell7.20e-1159
mesothelial cell5.23e-0919
endo-epithelial cell9.38e-0943
embryonic cell7.62e-07248
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.34e-17169
endoderm1.34e-17169
presumptive endoderm1.34e-17169
digestive system6.41e-17155
digestive tract6.41e-17155
primitive gut6.41e-17155
subdivision of digestive tract6.37e-16129
endodermal part of digestive tract6.37e-16129
endo-epithelium1.21e-1282
mixed endoderm/mesoderm-derived structure1.06e-11130
respiratory tract1.54e-1153
respiratory system6.77e-1172
gut epithelium1.24e-0954
segment of respiratory tract3.34e-0946
epithelial bud6.32e-0937
foregut1.18e-0898
orifice1.86e-0835
epithelial fold3.89e-0851
prostate gland9.67e-0811
male accessory sex gland9.67e-0811
embryonic cloacal epithelium9.67e-0811
epithelium of hindgut9.67e-0811
urogenital sinus epithelium9.67e-0811
prostate bud9.67e-0811
prostate field9.67e-0811
respiratory primordium2.18e-0738
endoderm of foregut2.18e-0738
cloaca4.56e-0714
anal region4.56e-0714
embryonic cloaca4.56e-0714
terminal part of digestive tract4.56e-0714
primitive urogenital sinus4.56e-0714
proctodeum4.56e-0714
sex gland6.93e-0712
male reproductive gland6.93e-0712
mesenchyme7.88e-07238
entire embryonic mesenchyme7.88e-07238
Disease
Ontology termp-valuen
carcinoma6.19e-15106
cell type cancer5.80e-13143
cancer1.28e-07235
disease of cellular proliferation1.68e-07239


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
EP300#203336.77394172622320.003216880500103790.01684133453057
FOXA1#3169311.08141974938550.000734755275698670.00584085144152027
FOXA2#3170216.42030916844350.004810682352105480.0226021347866096
MAFF#23764237.54357099329680.0009344774015560320.00677231873854073
MAFK#7975218.06715542521990.003983674744936810.0191191124804216
NR3C1#2908314.9730233311730.0002978331194675480.00310123560957839



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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