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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3759_papillotubular_clear_epidermoid_acantholytic_transitionalcell_rectal_mucinous
|full_id=C3759_papillotubular_clear_epidermoid_acantholytic_transitionalcell_rectal_mucinous
|id=C3759
|id=C3759

Revision as of 16:43, 12 September 2012


Full id: C3759_papillotubular_clear_epidermoid_acantholytic_transitionalcell_rectal_mucinous



Phase1 CAGE Peaks

Hg19::chr19:15939795..15939814,+p1@UCA1
Hg19::chr19:15939820..15939835,+p4@UCA1
Hg19::chr19:15939841..15939860,+p2@UCA1


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 cell4.56e-22254
endo-epithelial cell2.32e-1343
endodermal cell4.18e-1259
kidney tubule cell9.13e-0812
nephron tubule epithelial cell9.13e-0812
epithelial cell of alimentary canal2.99e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure7.72e-12169
endoderm7.72e-12169
presumptive endoderm7.72e-12169
renal system2.31e-1145
urinary system structure1.53e-1044
digestive system6.21e-10155
digestive tract6.21e-10155
primitive gut6.21e-10155
biliary system1.67e-097
biliary tree1.67e-097
biliary bud1.67e-097
larynx3.68e-099
reproductive structure3.70e-0959
reproductive system3.70e-0959
mixed endoderm/mesoderm-derived structure6.09e-09130
body cavity precursor2.11e-0863
intermediate mesoderm2.35e-0837
subdivision of digestive tract3.77e-08129
endodermal part of digestive tract3.77e-08129
mucosa4.07e-0812
duct4.35e-0826
renal tubule9.13e-0812
nephron tubule9.13e-0812
nephron tubule epithelium9.13e-0812
reproductive organ2.29e-0748
upper respiratory tract4.76e-0719
anatomical cavity5.91e-0770
cavitated compound organ6.70e-0732
Disease
Ontology termp-valuen
carcinoma3.19e-27106
cell type cancer3.05e-21143
cancer1.19e-14235
disease of cellular proliferation5.84e-14239
squamous cell carcinoma1.02e-1314
adenocarcinoma2.37e-1025


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#105137.971147625824820.001974187055288560.0115204851018205
ELF1#199734.258097958807540.01295179875054610.0462120498004265
EP300#203336.77394172622320.003216880500103790.0167431367761557
GATA1#2623313.56030814380040.0004009615963782630.00387848737280258
GATA2#2624312.7449317335540.0004829527704283790.00436853493770739
JUN#3725312.51282919233630.0005103313992726250.00444080161711662
JUND#372736.994663941871030.002921845042734990.0156722599978532
REST#597839.650028716128020.001112636247114590.0076726719717663
SIN3A#2594235.408884726815140.006318961977991520.0276625757647423
SPI1#668838.204323508522730.001810593189410520.0109045927056597
TAL1#6886329.86861667744023.75103522793067e-050.00071987204735364
TFAP2A#7020316.5186343730450.0002218033880766340.00248231076375221
TFAP2C#7022310.80922860986020.0007916746575753130.00615878655959092
USF1#739136.361499277207960.00388404057290560.0190202707081956
YY1#752834.911170749853860.008441455341808260.0329268778503497



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.