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Coexpression cluster:C3592: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3592_Fibroblast_schwannoma_basal_salivary_mesenchymal_large_Multipotent
|full_id=C3592_Fibroblast_schwannoma_basal_salivary_mesenchymal_large_Multipotent
|id=C3592
|id=C3592

Revision as of 16:32, 12 September 2012


Full id: C3592_Fibroblast_schwannoma_basal_salivary_mesenchymal_large_Multipotent



Phase1 CAGE Peaks

Hg19::chr16:82660560..82660585,+p1@CDH13
Hg19::chr16:82660594..82660607,+p3@CDH13
Hg19::chr16:82660635..82660650,+p2@CDH13


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
vasculature3.10e-1979
vascular system3.10e-1979
epithelium3.55e-19309
cell layer4.94e-19312
organism subdivision8.78e-19365
vessel3.22e-1869
anatomical cluster5.32e-18286
splanchnic layer of lateral plate mesoderm1.07e-1784
anatomical conduit2.56e-17241
multi-cellular organism1.64e-16659
circulatory system5.98e-16113
blood vessel8.36e-1660
epithelial tube open at both ends8.36e-1660
blood vasculature8.36e-1660
vascular cord8.36e-1660
cardiovascular system7.92e-15110
anatomical system2.85e-14625
somite4.08e-1483
paraxial mesoderm4.08e-1483
presomitic mesoderm4.08e-1483
presumptive segmental plate4.08e-1483
trunk paraxial mesoderm4.08e-1483
presumptive paraxial mesoderm4.08e-1483
anatomical group5.25e-14626
multilaminar epithelium7.97e-1482
multi-tissue structure7.35e-13347
epithelial tube9.79e-13118
dermomyotome2.00e-1270
skeletal muscle tissue8.10e-1261
striated muscle tissue8.10e-1261
myotome8.10e-1261
artery8.63e-1242
arterial blood vessel8.63e-1242
arterial system8.63e-1242
muscle tissue1.97e-1163
musculature1.97e-1163
musculature of body1.97e-1163
surface structure2.66e-1195
tube3.11e-11194
trunk mesenchyme4.98e-10143
systemic artery1.70e-0933
systemic arterial system1.70e-0933
primary circulatory organ3.98e-0927
unilaminar epithelium5.43e-09138
head2.49e-08123
compound organ5.22e-0869
heart7.16e-0824
primitive heart tube7.16e-0824
primary heart field7.16e-0824
anterior lateral plate mesoderm7.16e-0824
heart tube7.16e-0824
heart primordium7.16e-0824
cardiac mesoderm7.16e-0824
cardiogenic plate7.16e-0824
heart rudiment7.16e-0824
anterior region of body1.05e-07129
craniocervical region1.05e-07129
embryonic structure1.69e-07605
developing anatomical structure1.69e-07605
embryo2.19e-07612
germ layer2.51e-07604
embryonic tissue2.51e-07604
presumptive structure2.51e-07604
epiblast (generic)2.51e-07604
skin of body3.78e-0740
aorta3.78e-0721
aortic system3.78e-0721
ectoderm-derived structure4.27e-07169
integument4.46e-0745
integumental system4.46e-0745
Disease
Ontology termp-valuen
ovarian cancer5.27e-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
SUZ12#23512350.11578091106297.93834897779404e-060.000221974090734091



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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