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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate
|full_id=C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate
|id=C471
|id=C471

Revision as of 17:51, 12 September 2012


Full id: C471_Smooth_Fibroblast_leiomyoma_mesenchymal_Mesothelial_meningioma_Prostate



Phase1 CAGE Peaks

Hg19::chr8:42033234..42033247,-p@chr8:42033234..42033247
-
Hg19::chr8:42033253..42033264,-p@chr8:42033253..42033264
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Hg19::chr8:42033364..42033376,-p@chr8:42033364..42033376
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Hg19::chr8:42033383..42033398,-p@chr8:42033383..42033398
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Hg19::chr8:42033546..42033576,-p@chr8:42033546..42033576
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Hg19::chr8:42033578..42033605,-p@chr8:42033578..42033605
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Hg19::chr8:42033607..42033639,-p@chr8:42033607..42033639
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Hg19::chr8:42033640..42033671,-p@chr8:42033640..42033671
-
Hg19::chr8:42036444..42036460,+p@chr8:42036444..42036460
+
Hg19::chr8:42036539..42036561,-p@chr8:42036539..42036561
-
Hg19::chr8:42037500..42037536,-p@chr8:42037500..42037536
-
Hg19::chr8:42037883..42037900,-p@chr8:42037883..42037900
-
Hg19::chr8:42038055..42038068,-p3@PLAT
Hg19::chr8:42040287..42040298,-p10@PLAT
Hg19::chr8:42042635..42042650,-p4@PLAT
Hg19::chr8:42042654..42042665,-p9@PLAT
Hg19::chr8:42044953..42044969,-p@chr8:42044953..42044969
-
Hg19::chr8:42044977..42044996,-p@chr8:42044977..42044996
-
Hg19::chr8:42045498..42045512,-p6@PLAT
Hg19::chr8:42065075..42065090,-p1@PLAT
Hg19::chr8:42065187..42065201,-p2@PLAT


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
cell layer4.09e-29312
epithelium2.46e-28309
organism subdivision3.16e-26365
trunk mesenchyme5.16e-26143
multi-tissue structure2.61e-23347
somite1.36e-2283
paraxial mesoderm1.36e-2283
presomitic mesoderm1.36e-2283
presumptive segmental plate1.36e-2283
trunk paraxial mesoderm1.36e-2283
presumptive paraxial mesoderm1.36e-2283
multi-cellular organism5.09e-22659
epithelial tube9.33e-22118
dermomyotome1.55e-2170
multilaminar epithelium3.04e-2182
vasculature3.55e-2179
vascular system3.55e-2179
muscle tissue5.40e-2163
musculature5.40e-2163
musculature of body5.40e-2163
anatomical system1.02e-20625
skeletal muscle tissue1.40e-2061
striated muscle tissue1.40e-2061
myotome1.40e-2061
anatomical group1.58e-20626
splanchnic layer of lateral plate mesoderm3.26e-2084
trunk3.72e-20216
anatomical conduit1.43e-19241
anatomical cluster3.48e-19286
artery2.03e-1842
arterial blood vessel2.03e-1842
arterial system2.03e-1842
blood vessel4.02e-1860
epithelial tube open at both ends4.02e-1860
blood vasculature4.02e-1860
vascular cord4.02e-1860
vessel2.31e-1769
embryo3.77e-17612
embryonic structure4.85e-17605
developing anatomical structure4.85e-17605
germ layer9.13e-17604
embryonic tissue9.13e-17604
presumptive structure9.13e-17604
epiblast (generic)9.13e-17604
systemic artery1.83e-1633
systemic arterial system1.83e-1633
unilaminar epithelium1.89e-16138
tube2.14e-15194
cardiovascular system1.58e-14110
circulatory system3.20e-14113
mesenchyme1.97e-13238
entire embryonic mesenchyme1.97e-13238
compound organ4.19e-1169
aorta1.24e-0921
aortic system1.24e-0921
intermediate mesoderm2.03e-0937
urogenital ridge3.69e-0920
smooth muscle tissue4.78e-0915
organ1.02e-08511
mesonephros2.67e-0818
pronephros2.67e-0818
nephrogenic cord2.67e-0818
pronephric mesoderm2.67e-0818
rostral part of nephrogenic cord2.67e-0818
presumptive pronephric mesoderm2.67e-0818
excretory tube3.55e-0817
mesonephric epithelium3.55e-0817
mesonephric tubule3.55e-0817
nephric duct3.55e-0817
kidney epithelium3.55e-0817
renal duct3.55e-0817
mesonephric duct3.55e-0817
pronephric duct3.55e-0817
organ part6.05e-08219
nephron epithelium7.93e-0816
nephron7.93e-0816
uriniferous tubule7.93e-0816
metanephric mesenchyme7.93e-0816
nephrogenic mesenchyme7.93e-0816
mesoderm1.61e-07448


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
MEF2C#420835.901622070374860.01360717439201470.048017289036614



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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