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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3290_Endothelial_Retinal_Alveolar_thyroid_papillary_anaplastic_Ciliary
|full_id=C3290_Endothelial_Retinal_Alveolar_thyroid_papillary_anaplastic_Ciliary
|id=C3290
|id=C3290

Revision as of 16:11, 12 September 2012


Full id: C3290_Endothelial_Retinal_Alveolar_thyroid_papillary_anaplastic_Ciliary



Phase1 CAGE Peaks

Hg19::chr12:52626432..52626475,+p2@KRT7
Hg19::chr12:52626492..52626532,+p5@KRT7
Hg19::chr12:52626580..52626598,+p8@KRT7


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
anatomical space5.45e-13104
primordium8.02e-13168
simple squamous epithelium3.38e-1222
squamous epithelium8.74e-1225
immaterial anatomical entity1.22e-11126
endothelium1.85e-1118
blood vessel endothelium1.85e-1118
cardiovascular system endothelium1.85e-1118
anatomical cluster1.53e-10286
anatomical cavity2.87e-1070
epithelial tube3.15e-10118
vasculature5.99e-1079
vascular system5.99e-1079
body cavity precursor9.90e-1063
endoderm-derived structure1.28e-09169
endoderm1.28e-09169
presumptive endoderm1.28e-09169
trunk2.59e-09216
duct4.79e-0926
pigment epithelium of eye2.83e-0811
mesenchyme5.06e-08238
entire embryonic mesenchyme5.06e-08238
cell layer5.35e-08312
mixed endoderm/mesoderm-derived structure5.35e-08130
intermediate mesoderm7.26e-0837
respiratory tract8.11e-0853
unilaminar epithelium8.38e-08138
endothelial tube8.68e-089
arterial system endothelium8.68e-089
endothelium of artery8.68e-089
subdivision of trunk1.01e-07113
urogenital ridge1.14e-0720
epithelium1.39e-07309
multi-cellular organism3.16e-07659
organ segment3.26e-0797
mesonephros3.59e-0718
pronephros3.59e-0718
nephrogenic cord3.59e-0718
pronephric mesoderm3.59e-0718
rostral part of nephrogenic cord3.59e-0718
presumptive pronephric mesoderm3.59e-0718
respiratory primordium4.81e-0738
endoderm of foregut4.81e-0738
splanchnic layer of lateral plate mesoderm4.87e-0784
excretory tube5.41e-0717
mesonephric epithelium5.41e-0717
mesonephric tubule5.41e-0717
nephric duct5.41e-0717
kidney epithelium5.41e-0717
renal duct5.41e-0717
mesonephric duct5.41e-0717
pronephric duct5.41e-0717
vessel5.63e-0769
anatomical system5.66e-07625
extraembryonic membrane6.99e-0714
membranous layer6.99e-0714
nephron epithelium7.07e-0716
nephron7.07e-0716
uriniferous tubule7.07e-0716
metanephric mesenchyme7.07e-0716
nephrogenic mesenchyme7.07e-0716
anatomical group7.73e-07626


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
SMARCC1#6599343.66335931963151.20046018043203e-050.000301092364995535
TFAP2C#7022310.80922860986020.0007916746575753130.00613775588764814



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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