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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2837_liposarcoma_Fibroblast_Ewing_Olfactory_mesothelioma_Smooth_tenocyte
|full_id=C2837_liposarcoma_Fibroblast_Ewing_Olfactory_mesothelioma_Smooth_tenocyte
|id=C2837
|id=C2837

Revision as of 15:37, 12 September 2012


Full id: C2837_liposarcoma_Fibroblast_Ewing_Olfactory_mesothelioma_Smooth_tenocyte



Phase1 CAGE Peaks

Hg19::chr6:113697400..113697411,-p@chr6:113697400..113697411
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Hg19::chr6:113697530..113697541,-p@chr6:113697530..113697541
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Hg19::chr6:113697548..113697566,-p@chr6:113697548..113697566
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Hg19::chr6:113697568..113697589,-p@chr6:113697568..113697589
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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
somite2.76e-1483
paraxial mesoderm2.76e-1483
presomitic mesoderm2.76e-1483
presumptive segmental plate2.76e-1483
trunk paraxial mesoderm2.76e-1483
presumptive paraxial mesoderm2.76e-1483
artery1.40e-1142
arterial blood vessel1.40e-1142
arterial system1.40e-1142
surface structure9.10e-1195
dermomyotome7.54e-1070
vasculature1.64e-0979
vascular system1.64e-0979
systemic artery2.02e-0933
systemic arterial system2.02e-0933
splanchnic layer of lateral plate mesoderm2.25e-0984
multilaminar epithelium2.27e-0982
skeletal muscle tissue2.57e-0961
striated muscle tissue2.57e-0961
myotome2.57e-0961
blood vessel3.21e-0960
epithelial tube open at both ends3.21e-0960
blood vasculature3.21e-0960
vascular cord3.21e-0960
integument5.84e-0945
integumental system5.84e-0945
skin of body8.44e-0940
muscle tissue1.03e-0863
musculature1.03e-0863
musculature of body1.03e-0863
vessel1.56e-0869
skull3.16e-0811
cardiovascular system1.54e-07110
periodontium2.50e-076
dentition2.50e-076
trunk mesenchyme3.15e-07143
circulatory system5.10e-07113
aorta5.18e-0721
aortic system5.18e-0721
Disease
Ontology termp-valuen
musculoskeletal system disease4.95e-075
myotonic disease4.95e-075
muscle tissue disease4.95e-075
myopathy4.95e-075
muscular disease4.95e-075
myotonic dystrophy4.95e-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
EP300#203346.77394172622320.0004748459821442640.00435097732314132
FOS#235348.99795530889440.0001525147711168630.00195369682088483
MAFK#7975320.32554985337240.0001953213688931110.00235148915802047



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.