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Coexpression cluster:C2387

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Full id: C2387_kidney_renal_serous_smallcell_clear_mesothelioma_HES3GFP



Phase1 CAGE Peaks

Hg19::chr16:71879001..71879011,+p@chr16:71879001..71879011
+
Hg19::chr1:18807489..18807496,+p3@KLHDC7A
Hg19::chr1:18807498..18807518,+p1@KLHDC7A
Hg19::chr8:107593246..107593259,+p14@OXR1


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


GO IDGO nameFDR corrected p-value
GO:0016998cell wall catabolic process0.00339985870717061
GO:0007047cell wall organization and biogenesis0.00339985870717061
GO:0010382cell wall metabolic process0.00339985870717061
GO:0045229external encapsulating structure organization and biogenesis0.00339985870717061
GO:0006979response to oxidative stress0.0148357470858354



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
kidney tubule cell1.68e-1210
nephron tubule epithelial cell1.68e-1210
embryonic stem cell1.78e-125
kidney cell2.12e-1117
kidney epithelial cell2.12e-1117
epithelial cell2.65e-10253
endodermal cell2.72e-0858
epithelial cell of nephron6.25e-0815
Uber Anatomy
Ontology termp-valuen
kidney6.61e-1526
kidney mesenchyme6.61e-1526
upper urinary tract6.61e-1526
kidney rudiment6.61e-1526
kidney field6.61e-1526
abdomen element1.56e-1454
abdominal segment element1.56e-1454
cavitated compound organ7.09e-1431
urinary system structure1.73e-1347
renal system4.15e-1348
abdominal segment of trunk1.53e-1260
abdomen1.53e-1260
nephron tubule epithelium1.68e-1210
trunk region element1.79e-10101
epithelial sac8.41e-1025
excretory tube1.20e-0916
kidney epithelium1.20e-0916
sac2.47e-0926
epithelium of foregut-midgut junction4.12e-0825
anatomical boundary4.12e-0825
hepatobiliary system4.12e-0825
foregut-midgut junction4.12e-0825
septum transversum4.12e-0825
gut epithelium5.19e-0854
nephron epithelium6.25e-0815
renal tubule6.25e-0815
nephron tubule6.25e-0815
nephron6.25e-0815
uriniferous tubule6.25e-0815
nephrogenic mesenchyme6.25e-0815
hepatic diverticulum1.57e-0722
liver primordium1.57e-0722
subdivision of trunk3.32e-07112
digestive tract diverticulum3.95e-0723
endo-epithelium4.09e-0782
Disease
Ontology termp-valuen
carcinoma2.64e-11106
adenocarcinoma1.83e-1025
cell type cancer2.15e-07143
clear cell adenocarcinoma8.49e-072


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
BCL11A#53335214.18472755180350.007108328585298740.0296196428790303
CTBP2#1488231.35850016966410.001492676882047230.0095394493259167
ESR1#2099215.38430164807720.006065572629693510.0268367862686956
HNF4A#3172211.56614518147680.01057585681762490.0390666682055647
NANOG#79923214.62238924050630.006698757715363760.0284846527842871



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.