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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung
|full_id=C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung
|id=C1922
|id=C1922

Revision as of 14:33, 12 September 2012


Full id: C1922_renal_mesothelioma_serous_Renal_glioblastoma_Skeletal_lung



Phase1 CAGE Peaks

Hg19::chr3:149260161..149260281,-p2@WWTR1
Hg19::chr3:149260294..149260308,-p12@WWTR1
Hg19::chr3:149260318..149260331,-p14@WWTR1
Hg19::chr3:149260344..149260358,-p18@WWTR1
Hg19::chr3:149260370..149260390,-p21@WWTR1


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>

Cell Type
Ontology termp-valuen
mesodermal cell1.48e-28119
embryonic cell1.13e-16248
lining cell3.73e-1657
barrier cell3.73e-1657
endothelial cell of vascular tree7.94e-1524
non-terminally differentiated cell1.59e-14180
meso-epithelial cell2.85e-1444
endothelial cell1.59e-1235
contractile cell2.81e-1259
kidney cell1.42e-1118
kidney epithelial cell1.42e-1118
blood vessel endothelial cell1.89e-1118
embryonic blood vessel endothelial progenitor cell1.89e-1118
muscle precursor cell2.51e-1157
myoblast2.51e-1157
multi-potent skeletal muscle stem cell2.51e-1157
electrically responsive cell4.16e-1160
electrically active cell4.16e-1160
muscle cell9.17e-1154
epithelial cell of nephron3.09e-1016
vascular associated smooth muscle cell5.37e-0932
kidney cortical cell2.92e-0813
renal cortical epithelial cell2.92e-0813
kidney tubule cell3.63e-0812
nephron tubule epithelial cell3.63e-0812
epithelial cell3.91e-08254
smooth muscle cell4.19e-0842
smooth muscle myoblast4.19e-0842
Uber Anatomy
Ontology termp-valuen
epithelial tube1.89e-29118
epithelium1.66e-22309
cell layer1.79e-22312
trunk1.10e-21216
anatomical conduit1.25e-20241
splanchnic layer of lateral plate mesoderm2.65e-2084
tube4.65e-20194
vasculature5.06e-2079
vascular system5.06e-2079
anatomical cluster1.60e-19286
unilaminar epithelium2.07e-19138
trunk mesenchyme2.35e-19143
vessel1.62e-1869
blood vessel1.17e-1760
epithelial tube open at both ends1.17e-1760
blood vasculature1.17e-1760
vascular cord1.17e-1760
multi-tissue structure4.80e-15347
mesenchyme5.87e-15238
entire embryonic mesenchyme5.87e-15238
organism subdivision5.10e-14365
circulatory system6.42e-14113
cardiovascular system1.04e-13110
artery2.95e-1342
arterial blood vessel2.95e-1342
arterial system2.95e-1342
multi-cellular organism1.18e-12659
simple squamous epithelium2.15e-1222
muscle tissue2.52e-1263
musculature2.52e-1263
musculature of body2.52e-1263
duct6.79e-1226
skeletal muscle tissue7.39e-1261
striated muscle tissue7.39e-1261
myotome7.39e-1261
squamous epithelium1.00e-1125
compound organ1.19e-1169
endothelium1.89e-1118
blood vessel endothelium1.89e-1118
cardiovascular system endothelium1.89e-1118
anatomical system2.45e-11625
dermomyotome3.11e-1170
anatomical group4.01e-11626
mesonephros1.43e-1018
pronephros1.43e-1018
nephrogenic cord1.43e-1018
pronephric mesoderm1.43e-1018
rostral part of nephrogenic cord1.43e-1018
presumptive pronephric mesoderm1.43e-1018
systemic artery1.56e-1033
systemic arterial system1.56e-1033
excretory tube1.88e-1017
mesonephric epithelium1.88e-1017
mesonephric tubule1.88e-1017
nephric duct1.88e-1017
kidney epithelium1.88e-1017
renal duct1.88e-1017
mesonephric duct1.88e-1017
pronephric duct1.88e-1017
somite2.58e-1083
paraxial mesoderm2.58e-1083
presomitic mesoderm2.58e-1083
presumptive segmental plate2.58e-1083
trunk paraxial mesoderm2.58e-1083
presumptive paraxial mesoderm2.58e-1083
embryonic structure3.06e-10605
developing anatomical structure3.06e-10605
nephron epithelium3.09e-1016
nephron3.09e-1016
uriniferous tubule3.09e-1016


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
FOS#235358.99795530889441.69470025615156e-050.000389680317155907
GATA2#2624512.7449317335542.9719152914525e-060.000101267165130182
JUN#3725512.51282919233633.25800591331781e-060.000109233669207383
NR3C1#2908514.9730233311731.32777388277837e-065.25469407137135e-05



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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