Personal tools

Coexpression cluster:C1542


Revision as of 02:25, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C1542_Fibroblast_ductal_liposarcoma_large_normal_mesenchymal_Myoblast

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><br>

Cell Type
Ontology termp-valuen
skin fibroblast9.82e-1623
multi fate stem cell2.47e-14427
somatic stem cell2.25e-13433
stem cell3.69e-12441
muscle precursor cell4.35e-1158
multi-potent skeletal muscle stem cell4.35e-1158
non-terminally differentiated cell1.01e-10106
muscle cell2.52e-0955
connective tissue cell8.29e-09361
contractile cell2.15e-0859
somatic cell7.29e-08588
mesenchymal cell1.26e-07354
motile cell1.96e-07386
stromal cell2.29e-0728
electrically responsive cell2.92e-0761
electrically active cell2.92e-0761
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue2.21e-1473
presomitic mesoderm2.46e-1471
presumptive segmental plate2.46e-1471
trunk paraxial mesoderm2.46e-1471
paraxial mesoderm6.95e-1472
presumptive paraxial mesoderm6.95e-1472
entire embryonic mesenchyme1.30e-13160
epithelial vesicle5.10e-1278
multilaminar epithelium2.34e-1183
muscle tissue2.21e-1064
musculature of body2.21e-1064
integumental system3.25e-1046
connective tissue3.64e-10371
skeletal muscle tissue5.18e-1062
striated muscle tissue5.18e-1062
skin of body5.39e-1041
trunk mesenchyme1.14e-09122
surface structure3.05e-0999
multi-tissue structure4.94e-08342
future dermis5.56e-079
musculoskeletal system8.89e-07167

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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)


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.