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|full_id=C4317_renal_squamous_bile_glassy_epidermoid_epithelioid_malignant
 
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|id=C4317
 
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|ontology_enrichment_celltype=CL:0000066!6.53e-41!254;CL:0002076!2.20e-17!43;CL:0000223!5.03e-17!59;CL:0000076!7.46e-09!62;CL:0002251!1.66e-08!21;CL:0000063!2.15e-07!578
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|ontology_enrichment_disease=DOID:305!5.87e-41!106;DOID:0050687!5.77e-31!143;DOID:162!5.24e-20!235;DOID:14566!6.77e-19!239;DOID:1749!6.38e-14!14;DOID:299!3.83e-11!25
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|ontology_enrichment_uberon=UBERON:0004119!6.56e-25!169;UBERON:0000925!6.56e-25!169;UBERON:0006595!6.56e-25!169;UBERON:0000077!1.32e-21!130;UBERON:0001007!2.39e-20!155;UBERON:0001555!2.39e-20!155;UBERON:0007026!2.39e-20!155;UBERON:0001041!9.54e-19!98;UBERON:0004921!8.27e-18!129;UBERON:0004185!8.27e-18!129;UBERON:0001004!1.35e-15!72;UBERON:0000065!2.43e-14!53;UBERON:0000072!3.50e-13!46;UBERON:0008947!1.78e-12!38;UBERON:0003258!1.78e-12!38;UBERON:0001737!1.94e-10!9;UBERON:0005177!3.30e-10!107;UBERON:0005911!1.31e-09!82;UBERON:0000466!1.44e-09!126;UBERON:0001557!4.85e-09!19;UBERON:0003104!9.34e-09!238;UBERON:0009142!9.34e-09!238;UBERON:0001048!1.78e-08!168;UBERON:0000062!1.83e-08!511;UBERON:0000464!1.87e-08!104;UBERON:0002294!3.17e-08!7;UBERON:0001173!3.17e-08!7;UBERON:0004912!3.17e-08!7;UBERON:0000161!2.04e-07!35
 
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Revision as of 05:47, 21 May 2012


Full id: C4317_renal_squamous_bile_glassy_epidermoid_epithelioid_malignant



Phase1 CAGE Peaks

  Short description
Hg19::chr3:194040528..194040540,- p@chr3:194040528..194040540
-
Hg19::chr3:194040578..194040593,- p@chr3:194040578..194040593
-
Hg19::chr3:194040598..194040638,- p@chr3:194040598..194040638
-


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell6.53e-41254
endo-epithelial cell2.20e-1743
endodermal cell5.03e-1759
squamous epithelial cell7.46e-0962
epithelial cell of alimentary canal1.66e-0821
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.56e-25169
endoderm6.56e-25169
presumptive endoderm6.56e-25169
mixed endoderm/mesoderm-derived structure1.32e-21130
digestive system2.39e-20155
digestive tract2.39e-20155
primitive gut2.39e-20155
foregut9.54e-1998
subdivision of digestive tract8.27e-18129
endodermal part of digestive tract8.27e-18129
respiratory system1.35e-1572
respiratory tract2.43e-1453
segment of respiratory tract3.50e-1346
respiratory primordium1.78e-1238
endoderm of foregut1.78e-1238
larynx1.94e-109
trunk region element3.30e-10107
endo-epithelium1.31e-0982
immaterial anatomical entity1.44e-09126
upper respiratory tract4.85e-0919
mesenchyme9.34e-09238
entire embryonic mesenchyme9.34e-09238
primordium1.78e-08168
organ1.83e-08511
anatomical space1.87e-08104
biliary system3.17e-087
biliary tree3.17e-087
biliary bud3.17e-087
orifice2.04e-0735
Disease
Ontology termp-valuen
carcinoma5.87e-41106
cell type cancer5.77e-31143
cancer5.24e-20235
disease of cellular proliferation6.77e-19239
squamous cell carcinoma6.38e-1414
adenocarcinoma3.83e-1125


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.