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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1144_Meningeal_Fibroblast_mesenchymal_ductal_Smooth_Preadipocyte_Pericytes
|full_id=C1144_Meningeal_Fibroblast_mesenchymal_ductal_Smooth_Preadipocyte_Pericytes
|id=C1144
|id=C1144

Revision as of 13:37, 12 September 2012


Full id: C1144_Meningeal_Fibroblast_mesenchymal_ductal_Smooth_Preadipocyte_Pericytes



Phase1 CAGE Peaks

Hg19::chr11:60680190..60680212,+p@chr11:60680190..60680212
+
Hg19::chr11:60680219..60680235,+p@chr11:60680219..60680235
+
Hg19::chr11:60680237..60680241,+p@chr11:60680237..60680241
+
Hg19::chr11:60680267..60680270,+p@chr11:60680267..60680270
+
Hg19::chr3:146517344..146517356,+p@chr3:146517344..146517356
+
Hg19::chr9:6565432..6565460,-p2@GLDC
Hg19::chr9:6565462..6565475,-p5@GLDC


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
vasculature6.94e-2879
vascular system6.94e-2879
cardiovascular system1.25e-23110
circulatory system2.25e-22113
vessel2.47e-2169
somite1.68e-1883
paraxial mesoderm1.68e-1883
presomitic mesoderm1.68e-1883
presumptive segmental plate1.68e-1883
trunk paraxial mesoderm1.68e-1883
presumptive paraxial mesoderm1.68e-1883
splanchnic layer of lateral plate mesoderm2.00e-1884
blood vessel4.02e-1760
epithelial tube open at both ends4.02e-1760
blood vasculature4.02e-1760
vascular cord4.02e-1760
dermomyotome4.69e-1770
skeletal muscle tissue6.14e-1661
striated muscle tissue6.14e-1661
myotome6.14e-1661
artery1.06e-1542
arterial blood vessel1.06e-1542
arterial system1.06e-1542
muscle tissue5.40e-1563
musculature5.40e-1563
musculature of body5.40e-1563
systemic artery9.30e-1433
systemic arterial system9.30e-1433
anatomical cluster1.13e-12286
multilaminar epithelium2.27e-1282
cell layer4.67e-12312
epithelium9.87e-11309
anatomical conduit1.86e-10241
tube2.45e-10194
epithelial tube8.27e-10118
unilaminar epithelium3.24e-09138
aorta7.84e-0821
aortic system7.84e-0821
endothelium1.47e-0718
blood vessel endothelium1.47e-0718
cardiovascular system endothelium1.47e-0718
vasculature of head2.13e-0711
vasculature of organ2.13e-0711
trunk mesenchyme5.24e-07143


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.

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