Personal tools

Coexpression cluster:C1350


Revision as of 04:15, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C1350_neuroectodermal_neuroblastoma_Melanocyte_Smooth_leiomyoma_hepatoma_mesenchymal

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>

Uber Anatomy
Ontology termp-valuen
trunk mesenchyme3.02e-22143
epithelial tube4.32e-20118
vascular system9.60e-2079
organism subdivision6.36e-19365
blood vessel9.91e-1860
epithelial tube open at both ends9.91e-1860
blood vasculature9.91e-1860
vascular cord9.91e-1860
arterial blood vessel2.08e-1742
arterial system2.08e-1742
entire embryonic mesenchyme4.05e-16238
unilaminar epithelium4.79e-16138
paraxial mesoderm9.47e-1683
presomitic mesoderm9.47e-1683
presumptive segmental plate9.47e-1683
trunk paraxial mesoderm9.47e-1683
presumptive paraxial mesoderm9.47e-1683
systemic artery5.47e-1533
systemic arterial system5.47e-1533
splanchnic layer of lateral plate mesoderm8.35e-1584
multi-cellular organism1.40e-14659
multilaminar epithelium1.68e-1482
skeletal muscle tissue2.32e-1261
striated muscle tissue2.32e-1261
cell layer6.57e-12312
muscle tissue9.78e-1263
musculature of body9.78e-1263
multi-tissue structure2.30e-11347
surface structure4.56e-1195
cardiovascular system2.03e-10110
anatomical system5.73e-10625
anatomical conduit6.23e-10241
circulatory system7.33e-10113
anatomical group9.46e-10626
subdivision of trunk1.17e-09113
anatomical cluster2.97e-09286
aortic system1.16e-0821
integumental system1.32e-0745
blood vessel smooth muscle2.61e-0710
arterial system smooth muscle2.61e-0710
artery smooth muscle tissue2.61e-0710
aorta smooth muscle tissue2.61e-0710
organ component layer5.09e-0757
immaterial anatomical entity6.14e-07126
skin of body8.12e-0740

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.