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Coexpression cluster:C3172: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3172_Mesenchymal_Small_Renal_mature_Fibroblast_Urothelial_Endothelial
|full_id=C3172_Mesenchymal_Small_Renal_mature_Fibroblast_Urothelial_Endothelial
|id=C3172
|id=C3172

Revision as of 16:02, 12 September 2012


Full id: C3172_Mesenchymal_Small_Renal_mature_Fibroblast_Urothelial_Endothelial



Phase1 CAGE Peaks

Hg19::chr11:61658913..61658932,-p2@FADS3
Hg19::chr11:61658952..61658974,-p3@FADS3
Hg19::chr11:61659006..61659046,-p1@FADS3


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
vasculature2.46e-1779
vascular system2.46e-1779
vessel8.34e-1769
organism subdivision2.02e-15365
epithelium4.53e-14309
cell layer7.27e-14312
blood vessel1.16e-1360
epithelial tube open at both ends1.16e-1360
blood vasculature1.16e-1360
vascular cord1.16e-1360
splanchnic layer of lateral plate mesoderm1.99e-1284
epithelial tube2.44e-12118
anatomical conduit1.62e-11241
multilaminar epithelium2.31e-1182
circulatory system3.11e-11113
cardiovascular system4.24e-11110
anatomical cluster5.02e-11286
multi-cellular organism1.17e-10659
trunk mesenchyme2.18e-10143
somite2.52e-1083
paraxial mesoderm2.52e-1083
presomitic mesoderm2.52e-1083
presumptive segmental plate2.52e-1083
trunk paraxial mesoderm2.52e-1083
presumptive paraxial mesoderm2.52e-1083
trunk4.75e-10216
artery1.67e-0942
arterial blood vessel1.67e-0942
arterial system1.67e-0942
dermomyotome5.50e-0970
unilaminar epithelium1.25e-08138
anatomical system1.49e-08625
anatomical group2.43e-08626
surface structure2.84e-0895
tube4.12e-08194
skeletal muscle tissue4.29e-0861
striated muscle tissue4.29e-0861
myotome4.29e-0861
multi-tissue structure8.01e-08347
systemic artery9.02e-0833
systemic arterial system9.02e-0833
endothelium1.55e-0718
blood vessel endothelium1.55e-0718
cardiovascular system endothelium1.55e-0718
muscle tissue2.29e-0763
musculature2.29e-0763
musculature of body2.29e-0763
integument3.57e-0745
integumental system3.57e-0745
aorta9.56e-0721
aortic system9.56e-0721


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
E2F1#186934.907389214879320.008460985347239390.0323766844495048
ELF1#199734.258097958807540.01295179875054610.0460202398431015
IRF1#365937.63716375356390.002244692747297240.0127652309194107
NFYB#4801316.75979325353650.0002123649923296180.00245019746287152
SIN3A#2594235.408884726815140.006318961977991520.0275517083463222
SP1#666735.69838137814090.005403962701712170.0245523322140391
ZBTB7A#5134137.35190930787590.002516255860282270.0139650996807323



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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