Personal tools

Coexpression cluster:C4636

From FANTOM5_SSTAR

Revision as of 20:11, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4636_squamous_oral_Hep2_epidermoid_mesothelioma_mucinous_ductal



Phase1 CAGE Peaks

Hg19::chr7:101917447..101917479,+p4@CUX1
Hg19::chr7:101917482..101917507,+p6@CUX1
Hg19::chr7:101917509..101917520,+p9@CUX1


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 cell2.13e-31254
endodermal cell2.35e-1059
endo-epithelial cell5.59e-0943
mesothelial cell9.21e-0819
squamous epithelial cell3.86e-0762
animal cell7.51e-07679
eukaryotic cell7.51e-07679
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure7.99e-19169
endoderm7.99e-19169
presumptive endoderm7.99e-19169
digestive system1.89e-17155
digestive tract1.89e-17155
primitive gut1.89e-17155
subdivision of digestive tract6.14e-16129
endodermal part of digestive tract6.14e-16129
mixed endoderm/mesoderm-derived structure4.29e-15130
respiratory tract1.13e-1453
respiratory system1.95e-1472
segment of respiratory tract2.53e-1446
respiratory primordium2.77e-1438
endoderm of foregut2.77e-1438
larynx4.51e-129
foregut1.10e-1198
immaterial anatomical entity1.31e-09126
endo-epithelium3.58e-0982
mesenchyme4.99e-09238
entire embryonic mesenchyme4.99e-09238
anatomical space1.16e-08104
upper respiratory tract4.64e-0819
mucosa1.05e-0712
thoracic cavity element1.26e-0734
thoracic cavity1.26e-0734
trunk region element1.90e-07107
reproductive structure2.61e-0759
reproductive system2.61e-0759
thoracic segment organ3.02e-0735
multi-tissue structure5.64e-07347
primordium6.51e-07168
Disease
Ontology termp-valuen
carcinoma9.68e-37106
cell type cancer3.38e-29143
disease of cellular proliferation6.15e-22239
cancer6.86e-21235
squamous cell carcinoma8.41e-1314
adenocarcinoma3.15e-1025
disease of anatomical entity3.68e-0739
respiratory system cancer7.94e-0716


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


No analysis results for this cluster

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.