Personal tools

Coexpression cluster:C2125

From FANTOM5_SSTAR

Revision as of 14:20, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2125_gastric_signet_Lens_Ciliary_lung_Hepatocyte_kidney



Phase1 CAGE Peaks

Hg19::chr11:27494245..27494278,-p5@LGR4
Hg19::chr11:27494279..27494308,-p3@LGR4
Hg19::chr11:27494309..27494328,-p2@LGR4
Hg19::chr11:27494329..27494347,-p1@LGR4


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 cell1.21e-07254
Uber Anatomy
Ontology termp-valuen
organ9.96e-19511
multi-cellular organism6.30e-17659
multi-tissue structure8.15e-15347
anatomical system2.29e-13625
anatomical group3.49e-13626
embryo1.49e-12612
primordium3.63e-12168
embryonic structure2.86e-10605
developing anatomical structure2.86e-10605
germ layer4.70e-10604
embryonic tissue4.70e-10604
presumptive structure4.70e-10604
epiblast (generic)4.70e-10604
organism subdivision1.09e-09365
anatomical cluster5.85e-08286
compound organ8.94e-0869
organ part1.54e-07219
reproductive organ2.17e-0748
epithelium2.38e-07309
cell layer2.82e-07312
adult organism4.11e-07115
digestive system4.16e-07155
digestive tract4.16e-07155
primitive gut4.16e-07155
external genitalia4.34e-0722
endoderm-derived structure4.93e-07169
endoderm4.93e-07169
presumptive endoderm4.93e-07169
gonad5.26e-0721
indifferent external genitalia5.26e-0721
indifferent gonad5.26e-0721
gonad primordium5.26e-0721
mesenchyme8.52e-07238
entire embryonic mesenchyme8.52e-07238
anatomical cavity9.02e-0770
reproductive structure9.44e-0759
reproductive system9.44e-0759
ectoderm9.92e-07173
presumptive ectoderm9.92e-07173
Disease
Ontology termp-valuen
cell type cancer4.94e-11143
carcinoma1.73e-09106


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.