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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3347_Endothelial_acute_Hepatic_Renal_Lymphatic_large_CD14
|full_id=C3347_Endothelial_acute_Hepatic_Renal_Lymphatic_large_CD14
|id=C3347
|id=C3347

Revision as of 16:15, 12 September 2012


Full id: C3347_Endothelial_acute_Hepatic_Renal_Lymphatic_large_CD14



Phase1 CAGE Peaks

Hg19::chr12:96588368..96588394,+p3@ELK3
Hg19::chrX:71299606..71299619,+p@chrX:71299606..71299619
+
Hg19::chrX:71299620..71299649,+p@chrX:71299620..71299649
+


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
vessel4.60e-1969
vasculature6.32e-1979
vascular system6.32e-1979
circulatory system2.28e-16113
blood vessel1.02e-1560
epithelial tube open at both ends1.02e-1560
blood vasculature1.02e-1560
vascular cord1.02e-1560
splanchnic layer of lateral plate mesoderm1.09e-1584
cardiovascular system1.41e-15110
lateral plate mesoderm9.23e-14216
endothelium2.94e-1318
blood vessel endothelium2.94e-1318
cardiovascular system endothelium2.94e-1318
epithelial tube1.54e-12118
multi-cellular organism1.19e-11659
anatomical group1.65e-11626
anatomical system2.36e-11625
simple squamous epithelium1.28e-1022
embryo7.63e-10612
embryonic structure1.47e-09605
developing anatomical structure1.47e-09605
germ layer2.82e-09604
embryonic tissue2.82e-09604
presumptive structure2.82e-09604
epiblast (generic)2.82e-09604
artery7.88e-0942
arterial blood vessel7.88e-0942
arterial system7.88e-0942
squamous epithelium2.11e-0825
anatomical conduit2.89e-08241
mesoderm8.80e-08448
mesoderm-derived structure8.80e-08448
presumptive mesoderm8.80e-08448
anatomical cluster2.06e-07286
endothelial tube2.25e-079
arterial system endothelium2.25e-079
endothelium of artery2.25e-079


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#235338.99795530889440.001372499272417130.00895778349656121
TRIM28#10155212.39368336350830.008368344129438470.032896021248661



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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