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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4517_Smooth_mesenchymal_colon_Meningeal_large_Preadipocyte_Fibroblast
|full_id=C4517_Smooth_mesenchymal_colon_Meningeal_large_Preadipocyte_Fibroblast
|id=C4517
|id=C4517

Revision as of 17:36, 12 September 2012


Full id: C4517_Smooth_mesenchymal_colon_Meningeal_large_Preadipocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr5:72416387..72416409,+p1@TMEM171
Hg19::chr5:72416428..72416441,+p3@TMEM171
Hg19::chr5:72416466..72416490,+p2@TMEM171


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
artery7.08e-2342
arterial blood vessel7.08e-2342
arterial system7.08e-2342
vasculature3.57e-2179
vascular system3.57e-2179
splanchnic layer of lateral plate mesoderm1.22e-2084
vessel8.82e-2069
blood vessel1.07e-1960
epithelial tube open at both ends1.07e-1960
blood vasculature1.07e-1960
vascular cord1.07e-1960
multilaminar epithelium1.99e-1882
somite2.05e-1883
paraxial mesoderm2.05e-1883
presomitic mesoderm2.05e-1883
presumptive segmental plate2.05e-1883
trunk paraxial mesoderm2.05e-1883
presumptive paraxial mesoderm2.05e-1883
cell layer1.76e-17312
systemic artery2.08e-1733
systemic arterial system2.08e-1733
epithelial tube2.27e-17118
dermomyotome2.55e-1770
epithelium2.42e-16309
trunk mesenchyme1.53e-15143
unilaminar epithelium4.37e-15138
organism subdivision4.86e-14365
cardiovascular system6.37e-14110
muscle tissue1.27e-1363
musculature1.27e-1363
musculature of body1.27e-1363
skeletal muscle tissue1.38e-1361
striated muscle tissue1.38e-1361
myotome1.38e-1361
circulatory system5.15e-13113
trunk7.55e-13216
multi-tissue structure1.51e-12347
anatomical cluster3.02e-12286
multi-cellular organism9.96e-12659
anatomical system8.09e-11625
anatomical group1.40e-10626
aorta2.13e-1021
aortic system2.13e-1021
anatomical conduit2.24e-10241
tube2.79e-09194
mesenchyme3.10e-09238
entire embryonic mesenchyme3.10e-09238
blood vessel smooth muscle2.98e-0710
arterial system smooth muscle2.98e-0710
artery smooth muscle tissue2.98e-0710
aorta smooth muscle tissue2.98e-0710
endothelium3.71e-0718
blood vessel endothelium3.71e-0718
cardiovascular system endothelium3.71e-0718
skin of body4.93e-0740
embryo5.67e-07612
surface structure5.97e-0795
integument7.93e-0745
integumental system7.93e-0745
germ layer9.42e-07604
embryonic tissue9.42e-07604
presumptive structure9.42e-07604
epiblast (generic)9.42e-07604


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#186934.907389214879320.008460985347239390.03272318355356
MYC#460935.22228187160940.007020843755740150.0295748760136226



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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