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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast
|full_id=C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast
|id=C3412
|id=C3412

Revision as of 16:19, 12 September 2012


Full id: C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast



Phase1 CAGE Peaks

Hg19::chr14:23305848..23305863,+p3@MMP14
Hg19::chr14:23305868..23305889,+p4@MMP14
Hg19::chr14:23305909..23305918,+p5@MMP14


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
artery2.15e-2242
arterial blood vessel2.15e-2242
arterial system2.15e-2242
splanchnic layer of lateral plate mesoderm4.52e-2284
blood vessel1.31e-2160
epithelial tube open at both ends1.31e-2160
blood vasculature1.31e-2160
vascular cord1.31e-2160
vasculature2.04e-2179
vascular system2.04e-2179
multilaminar epithelium2.63e-2182
vessel2.02e-2069
somite9.36e-2083
paraxial mesoderm9.36e-2083
presomitic mesoderm9.36e-2083
presumptive segmental plate9.36e-2083
trunk paraxial mesoderm9.36e-2083
presumptive paraxial mesoderm9.36e-2083
dermomyotome4.95e-1970
epithelial tube1.05e-18118
skeletal muscle tissue3.35e-1861
striated muscle tissue3.35e-1861
myotome3.35e-1861
systemic artery4.90e-1833
systemic arterial system4.90e-1833
muscle tissue1.15e-1763
musculature1.15e-1763
musculature of body1.15e-1763
musculoskeletal system8.29e-17167
trunk mesenchyme2.73e-16143
mesoderm6.33e-16448
mesoderm-derived structure6.33e-16448
presumptive mesoderm6.33e-16448
multi-cellular organism1.17e-15659
unilaminar epithelium3.45e-15138
cardiovascular system6.03e-15110
circulatory system2.91e-14113
anatomical system7.01e-14625
lateral plate mesoderm1.11e-13216
anatomical group1.42e-13626
aorta1.41e-1121
aortic system1.41e-1121
trunk1.44e-11216
embryonic structure1.44e-11605
developing anatomical structure1.44e-11605
germ layer2.08e-11604
embryonic tissue2.08e-11604
presumptive structure2.08e-11604
epiblast (generic)2.08e-11604
embryo3.73e-11612
cell layer7.32e-09312
epithelium7.83e-09309
blood vessel smooth muscle2.93e-0710
arterial system smooth muscle2.93e-0710
artery smooth muscle tissue2.93e-0710
aorta smooth muscle tissue2.93e-0710
smooth muscle tissue5.77e-0715
Disease
Ontology termp-valuen
ovarian cancer1.56e-0714


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
CTBP2#1488362.71700033932814.049570681927e-060.000129258286201031
CTCF#1066435.360256373075030.0064925092527670.0278800696455628
MAFK#7975327.10073313782995.02195559325033e-050.000856866558084417
RAD21#5885310.35503389545630.0009004912073565420.0066276533618823



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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