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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3482_Fibroblast_Hair_Preadipocyte_Smooth_mesenchymal_Adipocyte_Keratocytes
|full_id=C3482_Fibroblast_Hair_Preadipocyte_Smooth_mesenchymal_Adipocyte_Keratocytes
|id=C3482
|id=C3482

Revision as of 16:25, 12 September 2012


Full id: C3482_Fibroblast_Hair_Preadipocyte_Smooth_mesenchymal_Adipocyte_Keratocytes



Phase1 CAGE Peaks

Hg19::chr15:39534820..39534834,+p@chr15:39534820..39534834
+
Hg19::chr1:215130919..215130936,+p@chr1:215130919..215130936
+
Hg19::chr8:119800776..119800782,+p@chr8:119800776..119800782
+


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>


Uber Anatomy
Ontology termp-valuen
somite1.74e-2183
paraxial mesoderm1.74e-2183
presomitic mesoderm1.74e-2183
presumptive segmental plate1.74e-2183
trunk paraxial mesoderm1.74e-2183
presumptive paraxial mesoderm1.74e-2183
multilaminar epithelium4.16e-1782
dermomyotome6.66e-1770
skeletal muscle tissue7.32e-1461
striated muscle tissue7.32e-1461
myotome7.32e-1461
systemic artery1.49e-1333
systemic arterial system1.49e-1333
muscle tissue4.33e-1363
musculature4.33e-1363
musculature of body4.33e-1363
artery8.61e-1342
arterial blood vessel8.61e-1342
arterial system8.61e-1342
surface structure1.62e-1295
trunk mesenchyme5.97e-12143
integument7.01e-1245
integumental system7.01e-1245
skin of body9.71e-1240
trunk2.54e-09216
splanchnic layer of lateral plate mesoderm3.86e-0884
blood vessel4.11e-0860
epithelial tube open at both ends4.11e-0860
blood vasculature4.11e-0860
vascular cord4.11e-0860
organism subdivision7.84e-08365
blood vessel smooth muscle1.42e-0710
arterial system smooth muscle1.42e-0710
artery smooth muscle tissue1.42e-0710
aorta smooth muscle tissue1.42e-0710
periodontium4.35e-076
dentition4.35e-076
connective tissue7.17e-07375
Disease
Ontology termp-valuen
musculoskeletal system disease1.43e-075
myotonic disease1.43e-075
muscle tissue disease1.43e-075
myopathy1.43e-075
muscular disease1.43e-075
myotonic dystrophy1.43e-075


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


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

TF#promotersEnrichmentp-valueq-value
MAFK#7975218.06715542521990.003983674744936810.0191085751474971



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.