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Coexpression cluster:C4458: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280821326037329
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280821326037329
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4458_small_renal_kidney_Hepatocyte_clear_colon_argyrophil



Phase1 CAGE Peaks

Hg19::chr5:125706998..125707018,+p4@GRAMD3
Hg19::chr5:125707019..125707032,+p16@GRAMD3
Hg19::chr6:116381918..116381977,-p1@FRK


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
subdivision of digestive tract6.59e-27118
endoderm-derived structure8.13e-27160
endoderm8.13e-27160
presumptive endoderm8.13e-27160
abdomen element3.77e-2354
abdominal segment element3.77e-2354
digestive system3.44e-22145
digestive tract3.44e-22145
primitive gut3.44e-22145
renal system1.66e-2148
abdominal segment of trunk3.58e-2160
abdomen3.58e-2160
trunk region element1.71e-20101
urinary system structure2.06e-2047
epithelium of foregut-midgut junction1.49e-1525
anatomical boundary1.49e-1525
hepatobiliary system1.49e-1525
foregut-midgut junction1.49e-1525
septum transversum1.49e-1525
cavitated compound organ3.96e-1531
kidney4.26e-1526
kidney mesenchyme4.26e-1526
upper urinary tract4.26e-1526
kidney rudiment4.26e-1526
kidney field4.26e-1526
subdivision of trunk7.64e-15112
endo-epithelium9.71e-1582
sac2.42e-1426
gastrointestinal system4.87e-1425
foregut9.37e-1487
epithelial sac3.53e-1325
digestive tract diverticulum4.69e-1323
intestine1.42e-1217
gut epithelium1.44e-1254
immaterial anatomical entity1.68e-12117
larynx1.96e-129
excretory tube2.91e-1216
kidney epithelium2.91e-1216
nephron tubule epithelium5.30e-1210
hepatic diverticulum6.86e-1222
liver primordium6.86e-1222
trunk8.13e-12199
nephron epithelium7.24e-1115
renal tubule7.24e-1115
nephron tubule7.24e-1115
nephron7.24e-1115
uriniferous tubule7.24e-1115
nephrogenic mesenchyme7.24e-1115
mesenchyme4.25e-10160
entire embryonic mesenchyme4.25e-10160
hindgut5.35e-1019
organ system subdivision9.60e-10223
multi-tissue structure4.38e-09342
cortex of kidney4.67e-0912
renal parenchyma4.67e-0912
respiratory primordium1.37e-0838
endoderm of foregut1.37e-0838
duct1.62e-0819
organ2.73e-08503
liver2.85e-0819
digestive gland2.85e-0819
liver bud2.85e-0819
respiratory tract3.82e-0854
intermediate mesoderm4.10e-0828
anatomical cluster5.00e-08373
reproductive structure1.33e-0759
reproductive system1.33e-0759
large intestine3.52e-0711
internal genitalia4.60e-0725
cortex6.92e-0715
parenchyma6.92e-0715
small intestine7.41e-074
biliary system8.69e-079
biliary tree8.69e-079
biliary bud8.69e-079
Disease
Ontology termp-valuen
carcinoma2.80e-19106
cell type cancer4.79e-14143
adenocarcinoma1.59e-1325


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
CTCF#1066435.360256373075030.0064925092527670.0280821326037329



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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