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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4277_mesothelioma_Smooth_normal_Prostate_Ewing_thyroid_glioblastoma
|full_id=C4277_mesothelioma_Smooth_normal_Prostate_Ewing_thyroid_glioblastoma
|id=C4277
|id=C4277

Revision as of 17:20, 12 September 2012


Full id: C4277_mesothelioma_Smooth_normal_Prostate_Ewing_thyroid_glioblastoma



Phase1 CAGE Peaks

Hg19::chr3:124829277..124829294,-p10@SLC12A8
Hg19::chr3:124829396..124829423,-p3@SLC12A8
Hg19::chr3:124829429..124829456,-p1@SLC12A8


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.07e-28180
fibroblast1.60e-2075
animal cell3.40e-19679
eukaryotic cell3.40e-19679
somatic cell4.28e-18591
multi fate stem cell2.69e-15430
somatic stem cell2.11e-14436
stem cell3.36e-13444
native cell6.35e-12722
connective tissue cell8.00e-11365
motile cell2.12e-09390
mesenchymal cell4.18e-09358
contractile cell1.31e-0859
muscle precursor cell3.68e-0857
myoblast3.68e-0857
multi-potent skeletal muscle stem cell3.68e-0857
muscle cell7.77e-0854
mesothelial cell1.74e-0719
mesodermal cell8.72e-07119
Uber Anatomy
Ontology termp-valuen
connective tissue5.31e-11375
somite2.81e-0983
paraxial mesoderm2.81e-0983
presomitic mesoderm2.81e-0983
presumptive segmental plate2.81e-0983
trunk paraxial mesoderm2.81e-0983
presumptive paraxial mesoderm2.81e-0983
trunk mesenchyme2.44e-07143
vasculature of head3.63e-0711
vasculature of organ3.63e-0711
dermomyotome4.85e-0770
anterior segment of eyeball7.28e-0714
skeletal muscle tissue9.08e-0761
striated muscle tissue9.08e-0761
myotome9.08e-0761
Disease
Ontology termp-valuen
ovarian cancer3.95e-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
EP300#203336.77394172622320.003216880500103790.0167916724585336
FOS#235338.99795530889440.001372499272417130.00899827065360782
JUN#3725312.51282919233630.0005103313992726250.00445192958642112
JUNB#3726330.61063265982113.4847716247536e-050.000681419329184875
JUND#372736.994663941871030.002921845042734990.0157182741536108
RAD21#5885310.35503389545630.0009004912073565420.00666286937336945
STAT3#6774310.51946499715420.0008589184530415310.00644151833385067



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.