Personal tools

Coexpression cluster:C4728


Revision as of 05:52, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C4728_immature_Gingival_malignant_epidermoid_esophagus_spleen_Mallassezderived

Phase1 CAGE Peaks


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>

Uber Anatomy
Ontology termp-valuen
respiratory system1.29e-1272
endoderm-derived structure4.27e-11169
presumptive endoderm4.27e-11169
blood vessel endothelium4.17e-1018
cardiovascular system endothelium4.17e-1018
anatomical system9.11e-10625
anatomical group1.12e-09626
respiratory tract2.29e-0953
embryonic structure5.97e-09605
developing anatomical structure5.97e-09605
endothelial tube6.66e-099
arterial system endothelium6.66e-099
endothelium of artery6.66e-099
simple squamous epithelium1.13e-0822
germ layer1.20e-08604
embryonic tissue1.20e-08604
presumptive structure1.20e-08604
epiblast (generic)1.20e-08604
multi-cellular organism1.21e-08659
oral opening1.58e-0821
squamous epithelium3.45e-0825
digestive system3.87e-08155
digestive tract3.87e-08155
primitive gut3.87e-08155
mixed endoderm/mesoderm-derived structure2.39e-07130
mesoderm-derived structure5.58e-07448
presumptive mesoderm5.58e-07448
Ontology termp-valuen
squamous cell carcinoma2.17e-1014

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



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.