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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2298_pagetoid_liposarcoma_mesothelioma_mucinous_epidermoid_large_bile
|full_id=C2298_pagetoid_liposarcoma_mesothelioma_mucinous_epidermoid_large_bile
|id=C2298
|id=C2298

Revision as of 15:00, 12 September 2012


Full id: C2298_pagetoid_liposarcoma_mesothelioma_mucinous_epidermoid_large_bile



Phase1 CAGE Peaks

Hg19::chr14:52021357..52021368,+p13@FRMD6
Hg19::chr14:52021378..52021407,+p3@FRMD6
Hg19::chr14:52021408..52021419,+p8@FRMD6
Hg19::chr14:52021434..52021439,+p22@FRMD6


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
somite6.59e-1983
paraxial mesoderm6.59e-1983
presomitic mesoderm6.59e-1983
presumptive segmental plate6.59e-1983
trunk paraxial mesoderm6.59e-1983
presumptive paraxial mesoderm6.59e-1983
trunk mesenchyme1.57e-17143
multilaminar epithelium8.44e-1682
dermomyotome9.18e-1670
skeletal muscle tissue3.11e-1361
striated muscle tissue3.11e-1361
myotome3.11e-1361
trunk2.17e-12216
muscle tissue2.70e-1263
musculature2.70e-1263
musculature of body2.70e-1263
surface structure2.08e-1195
organism subdivision4.93e-11365
unilaminar epithelium1.75e-10138
artery1.98e-1042
arterial blood vessel1.98e-1042
arterial system1.98e-1042
systemic artery1.65e-0933
systemic arterial system1.65e-0933
skin of body2.82e-0940
integument3.10e-0945
integumental system3.10e-0945
vasculature4.31e-0879
vascular system4.31e-0879
splanchnic layer of lateral plate mesoderm8.22e-0884
mesenchyme9.28e-08238
entire embryonic mesenchyme9.28e-08238
epithelial tube1.00e-07118
blood vessel1.47e-0760
epithelial tube open at both ends1.47e-0760
blood vasculature1.47e-0760
vascular cord1.47e-0760
blood vessel smooth muscle2.42e-0710
arterial system smooth muscle2.42e-0710
artery smooth muscle tissue2.42e-0710
aorta smooth muscle tissue2.42e-0710
vessel9.65e-0769


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
EP300#203346.77394172622320.0004748459821442640.00433689895314078
FOS#235348.99795530889440.0001525147711168630.00194605866593452
JUN#3725412.51282919233634.07770316866756e-050.000741935960335316
JUND#372746.994663941871030.000417684217818580.00391128145115706
PRDM1#6394131.8309557774613.29673728703385e-092.72395526519405e-07



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.