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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4086_Smooth_Mesothelial_seminal_Fibroblast_Alveolar_Melanocyte_Preadipocyte
|full_id=C4086_Smooth_Mesothelial_seminal_Fibroblast_Alveolar_Melanocyte_Preadipocyte
|id=C4086
|id=C4086

Revision as of 17:07, 12 September 2012


Full id: C4086_Smooth_Mesothelial_seminal_Fibroblast_Alveolar_Melanocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr22:18105870..18105871,-p@chr22:18105870..18105871
-
Hg19::chr7:27163592..27163605,-p@chr7:27163592..27163605
-
Hg19::chr8:90556171..90556173,+p@chr8:90556171..90556173
+


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
artery3.86e-1442
arterial blood vessel3.86e-1442
arterial system3.86e-1442
systemic artery1.74e-1333
systemic arterial system1.74e-1333
skeletal muscle tissue2.93e-1161
striated muscle tissue2.93e-1161
myotome2.93e-1161
muscle tissue1.39e-1063
musculature1.39e-1063
musculature of body1.39e-1063
blood vessel9.69e-1060
epithelial tube open at both ends9.69e-1060
blood vasculature9.69e-1060
vascular cord9.69e-1060
trunk4.05e-09216
vasculature5.20e-0979
vascular system5.20e-0979
vessel1.03e-0869
dermomyotome1.46e-0870
mesenchyme2.07e-08238
entire embryonic mesenchyme2.07e-08238
somite2.76e-0883
paraxial mesoderm2.76e-0883
presomitic mesoderm2.76e-0883
presumptive segmental plate2.76e-0883
trunk paraxial mesoderm2.76e-0883
presumptive paraxial mesoderm2.76e-0883
epithelial tube3.95e-08118
blood vessel smooth muscle6.96e-0810
arterial system smooth muscle6.96e-0810
artery smooth muscle tissue6.96e-0810
aorta smooth muscle tissue6.96e-0810
trunk mesenchyme3.09e-07143
organism subdivision5.86e-07365


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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