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Coexpression cluster:C4540: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.01156766841715!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168236245643635!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583552138697288
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.01156766841715!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168236245643635!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583552138697288
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}}
}}

Revision as of 16:48, 26 November 2012


Full id: C4540_serous_renal_Hepatocyte_signet_gall_liver_kidney



Phase1 CAGE Peaks

Hg19::chr6:107235234..107235237,-p3@LOC100422737
Hg19::chr6:107235249..107235267,-p1@LOC100422737
Hg19::chr6:107235287..107235303,-p2@LOC100422737


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
epithelium of foregut-midgut junction7.26e-2325
anatomical boundary7.26e-2325
hepatobiliary system7.26e-2325
foregut-midgut junction7.26e-2325
septum transversum7.26e-2325
abdomen element1.09e-2254
abdominal segment element1.09e-2254
hepatic diverticulum4.02e-2122
liver primordium4.02e-2122
digestive tract diverticulum3.85e-2023
abdominal segment of trunk4.12e-2060
abdomen4.12e-2060
liver1.16e-1919
digestive gland1.16e-1919
liver bud1.16e-1919
epithelial sac2.06e-1825
sac1.20e-1726
trunk region element3.64e-14101
gut epithelium1.16e-1154
exocrine gland1.34e-1131
exocrine system1.34e-1131
subdivision of trunk8.34e-11112
endocrine gland3.88e-1035
endocrine system1.08e-0945
renal cortex tubule6.47e-093
region of nephron tubule6.47e-093
proximal tubule6.47e-093
endo-epithelium1.98e-0882
kidney4.46e-0826
kidney mesenchyme4.46e-0826
upper urinary tract4.46e-0826
kidney rudiment4.46e-0826
kidney field4.46e-0826
epithelium of female gonad6.59e-081
immaterial anatomical entity1.70e-07117
vas deferens3.62e-071
spermatic cord3.62e-071
uterus or analog4.61e-071
Disease
Ontology termp-valuen
ovary epithelial cancer6.59e-081
carcinoma3.30e-07106
disease of anatomical entity8.14e-0739


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)

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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
CEBPB#105137.971147625824820.001974187055288560.01156766841715
EP300#203336.77394172622320.003216880500103790.0168236245643635
FOXA1#3169311.08141974938550.000734755275698670.00583552138697288



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.