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Coexpression cluster:C4277: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167916724585336!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899827065360782!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445192958642112!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000681419329184875!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157182741536108!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666286937336945!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644151833385067
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167916724585336!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899827065360782!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445192958642112!JUNB#3726;3:30.6106326598211:3.4847716247536e-05:0.000681419329184875!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157182741536108!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666286937336945!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644151833385067
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}}
}}

Revision as of 16:39, 26 November 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
fibroblast3.67e-1976
animal cell1.40e-15679
eukaryotic cell1.40e-15679
somatic cell2.03e-15588
multi fate stem cell3.93e-12427
somatic stem cell2.28e-11433
native cell1.86e-10722
stem cell2.12e-10441
connective tissue cell6.23e-09361
motile cell8.20e-09386
mesenchymal cell9.92e-08354
contractile cell1.94e-0759
mesothelial cell1.97e-0719
non-terminally differentiated cell2.53e-07106
muscle precursor cell7.54e-0758
myoblast7.54e-0758
multi-potent skeletal muscle stem cell7.54e-0758
Uber Anatomy
Ontology termp-valuen
connective tissue1.94e-09371
anterior segment of eyeball5.64e-0814
vasculature of organ1.51e-0711
subdivision of head3.34e-0749
Disease
Ontology termp-valuen
ovarian cancer2.48e-0814


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.