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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial
|full_id=C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial
|id=C1844
|id=C1844

Revision as of 14:28, 12 September 2012


Full id: C1844_squamous_epidermoid_bronchioalveolar_Corneal_Alveolar_Esophageal_Urothelial



Phase1 CAGE Peaks

Hg19::chr1:207205989..207206000,-p4@C1orf116
Hg19::chr1:207206001..207206012,-p5@C1orf116
Hg19::chr1:207206020..207206050,-p1@C1orf116
Hg19::chr1:207206095..207206121,-p2@C1orf116
Hg19::chr1:59042917..59042931,-p1@TACSTD2


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 cell1.41e-31254
endo-epithelial cell1.68e-1643
endodermal cell1.63e-1359
respiratory epithelial cell1.00e-0713
epithelial cell of alimentary canal2.39e-0721
kidney cell5.69e-0718
kidney epithelial cell5.69e-0718
epithelial cell of nephron7.74e-0716
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.77e-18169
endoderm4.77e-18169
presumptive endoderm4.77e-18169
anatomical space6.39e-15104
immaterial anatomical entity1.24e-14126
respiratory system9.43e-1472
digestive system4.05e-13155
digestive tract4.05e-13155
primitive gut4.05e-13155
multi-cellular organism4.22e-12659
mixed endoderm/mesoderm-derived structure1.37e-11130
subdivision of digestive tract1.44e-11129
endodermal part of digestive tract1.44e-11129
anatomical system5.36e-11625
anatomical group8.47e-11626
respiratory tract2.31e-1053
anatomical cavity1.82e-0970
organ2.39e-09511
endo-epithelium4.68e-0982
renal system5.70e-0945
urinary system structure1.30e-0844
mesoderm1.41e-08448
mesoderm-derived structure1.41e-08448
presumptive mesoderm1.41e-08448
subdivision of trunk1.89e-08113
foregut1.93e-0898
embryo1.96e-08612
respiratory primordium5.43e-0838
endoderm of foregut5.43e-0838
orifice7.13e-0835
duct1.06e-0726
mesonephros1.71e-0718
pronephros1.71e-0718
nephrogenic cord1.71e-0718
pronephric mesoderm1.71e-0718
rostral part of nephrogenic cord1.71e-0718
presumptive pronephric mesoderm1.71e-0718
embryonic structure1.90e-07605
developing anatomical structure1.90e-07605
trunk region element2.17e-07107
reproductive structure2.81e-0759
reproductive system2.81e-0759
body cavity precursor3.17e-0763
segment of respiratory tract3.23e-0746
germ layer3.27e-07604
embryonic tissue3.27e-07604
presumptive structure3.27e-07604
epiblast (generic)3.27e-07604
excretory tube3.74e-0717
mesonephric epithelium3.74e-0717
mesonephric tubule3.74e-0717
nephric duct3.74e-0717
kidney epithelium3.74e-0717
renal duct3.74e-0717
mesonephric duct3.74e-0717
pronephric duct3.74e-0717
urogenital ridge4.63e-0720
epithelial bud5.23e-0737
nephron epithelium7.74e-0716
nephron7.74e-0716
uriniferous tubule7.74e-0716
metanephric mesenchyme7.74e-0716
nephrogenic mesenchyme7.74e-0716
Disease
Ontology termp-valuen
carcinoma1.62e-13106
squamous cell carcinoma9.31e-0914
adenocarcinoma6.63e-0725


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#105146.376918100659850.001113944176677320.00765591049407753
ELF1#199743.406478367046030.01235066105299550.0447381621016161
IRF1#365946.109731002851120.001315525264767990.00881057734558833
JUND#372745.595731153496820.001849593301755460.0109357832224886
MYC#460944.177825497287520.005691969036823440.0256865382291321
NFYA#4800414.74046455986444.14733626928016e-050.000752377371247786
NFYB#4801413.40783460282926.03169250119439e-050.00099156923206712
SP1#666744.558705102512720.00407573565781680.0194884056572992
TBP#690853.706770687096390.001428755106721120.0091933802347882



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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