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Coexpression cluster:C4569: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.79e-21!106;DOID:0050687!4.38e-17!143;DOID:1749!8.39e-08!14;DOID:162!1.61e-07!235;DOID:7!1.96e-07!39;DOID:14566!8.24e-07!239
|ontology_enrichment_disease=DOID:305!1.79e-21!106;DOID:0050687!4.38e-17!143;DOID:1749!8.39e-08!14;DOID:162!1.61e-07!235;DOID:7!1.96e-07!39;DOID:14566!8.24e-07!239
|ontology_enrichment_uberon=UBERON:0004119!1.09e-32!169;UBERON:0000925!1.09e-32!169;UBERON:0006595!1.09e-32!169;UBERON:0004921!1.57e-26!129;UBERON:0004185!1.57e-26!129;UBERON:0001007!2.98e-26!155;UBERON:0001555!2.98e-26!155;UBERON:0007026!2.98e-26!155;UBERON:0000077!5.24e-25!130;UBERON:0001041!5.62e-19!98;UBERON:0005911!2.86e-17!82;UBERON:0001004!2.03e-13!72;UBERON:0005177!2.84e-12!107;UBERON:0000062!7.73e-12!511;UBERON:0000065!8.21e-12!53;UBERON:0002530!9.67e-12!59;UBERON:0000481!3.45e-11!347;UBERON:0000466!4.01e-11!126;UBERON:0003929!4.29e-10!54;UBERON:0005157!1.39e-09!51;UBERON:0005153!3.22e-09!37;UBERON:0003104!7.68e-09!238;UBERON:0009142!7.68e-09!238;UBERON:0008947!7.75e-09!38;UBERON:0003258!7.75e-09!38;UBERON:0001048!8.00e-09!168;UBERON:0000064!9.25e-09!219;UBERON:0000072!2.21e-08!46;UBERON:0000161!2.22e-08!35;UBERON:0000468!4.85e-08!659;UBERON:0002365!1.06e-07!31;UBERON:0002330!1.06e-07!31;UBERON:0009856!1.51e-07!26;UBERON:0000475!2.35e-07!365;UBERON:0000467!2.61e-07!625;UBERON:0009569!2.62e-07!113;UBERON:0000464!2.90e-07!104;UBERON:0000063!2.97e-07!97;UBERON:0007499!3.16e-07!25;UBERON:0000480!3.38e-07!626;UBERON:0000477!4.58e-07!286;UBERON:0009497!6.87e-07!25;UBERON:0000015!6.87e-07!25;UBERON:0002423!6.87e-07!25;UBERON:0006235!6.87e-07!25;UBERON:0004161!6.87e-07!25
|ontology_enrichment_uberon=UBERON:0004119!1.09e-32!169;UBERON:0000925!1.09e-32!169;UBERON:0006595!1.09e-32!169;UBERON:0004921!1.57e-26!129;UBERON:0004185!1.57e-26!129;UBERON:0001007!2.98e-26!155;UBERON:0001555!2.98e-26!155;UBERON:0007026!2.98e-26!155;UBERON:0000077!5.24e-25!130;UBERON:0001041!5.62e-19!98;UBERON:0005911!2.86e-17!82;UBERON:0001004!2.03e-13!72;UBERON:0005177!2.84e-12!107;UBERON:0000062!7.73e-12!511;UBERON:0000065!8.21e-12!53;UBERON:0002530!9.67e-12!59;UBERON:0000481!3.45e-11!347;UBERON:0000466!4.01e-11!126;UBERON:0003929!4.29e-10!54;UBERON:0005157!1.39e-09!51;UBERON:0005153!3.22e-09!37;UBERON:0003104!7.68e-09!238;UBERON:0009142!7.68e-09!238;UBERON:0008947!7.75e-09!38;UBERON:0003258!7.75e-09!38;UBERON:0001048!8.00e-09!168;UBERON:0000064!9.25e-09!219;UBERON:0000072!2.21e-08!46;UBERON:0000161!2.22e-08!35;UBERON:0000468!4.85e-08!659;UBERON:0002365!1.06e-07!31;UBERON:0002330!1.06e-07!31;UBERON:0009856!1.51e-07!26;UBERON:0000475!2.35e-07!365;UBERON:0000467!2.61e-07!625;UBERON:0009569!2.62e-07!113;UBERON:0000464!2.90e-07!104;UBERON:0000063!2.97e-07!97;UBERON:0007499!3.16e-07!25;UBERON:0000480!3.38e-07!626;UBERON:0000477!4.58e-07!286;UBERON:0009497!6.87e-07!25;UBERON:0000015!6.87e-07!25;UBERON:0002423!6.87e-07!25;UBERON:0006235!6.87e-07!25;UBERON:0004161!6.87e-07!25
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}}
}}

Revision as of 13:08, 5 September 2012


Full id: C4569_placenta_mesothelioma_liposarcoma_rectal_prostate_Intestinal_adrenal



Phase1 CAGE Peaks

Hg19::chr6:142623708..142623713,+p8@GPR126
Hg19::chr6:142623784..142623795,+p5@GPR126
Hg19::chr6:142623806..142623820,+p2@GPR126


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
epithelial cell2.13e-38254
endodermal cell1.04e-1659
endo-epithelial cell3.01e-1243
squamous epithelial cell3.01e-1262
mesothelial cell6.65e-1019
epithelial cell of alimentary canal4.82e-0721
respiratory epithelial cell6.39e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.09e-32169
endoderm1.09e-32169
presumptive endoderm1.09e-32169
subdivision of digestive tract1.57e-26129
endodermal part of digestive tract1.57e-26129
digestive system2.98e-26155
digestive tract2.98e-26155
primitive gut2.98e-26155
mixed endoderm/mesoderm-derived structure5.24e-25130
foregut5.62e-1998
endo-epithelium2.86e-1782
respiratory system2.03e-1372
trunk region element2.84e-12107
organ7.73e-12511
respiratory tract8.21e-1253
gland9.67e-1259
multi-tissue structure3.45e-11347
immaterial anatomical entity4.01e-11126
gut epithelium4.29e-1054
epithelial fold1.39e-0951
epithelial bud3.22e-0937
mesenchyme7.68e-09238
entire embryonic mesenchyme7.68e-09238
respiratory primordium7.75e-0938
endoderm of foregut7.75e-0938
primordium8.00e-09168
organ part9.25e-09219
segment of respiratory tract2.21e-0846
orifice2.22e-0835
multi-cellular organism4.85e-08659
exocrine gland1.06e-0731
exocrine system1.06e-0731
sac1.51e-0726
organism subdivision2.35e-07365
anatomical system2.61e-07625
subdivision of trunk2.62e-07113
anatomical space2.90e-07104
organ segment2.97e-0797
epithelial sac3.16e-0725
anatomical group3.38e-07626
anatomical cluster4.58e-07286
epithelium of foregut-midgut junction6.87e-0725
anatomical boundary6.87e-0725
hepatobiliary system6.87e-0725
foregut-midgut junction6.87e-0725
septum transversum6.87e-0725
Disease
Ontology termp-valuen
carcinoma1.79e-21106
cell type cancer4.38e-17143
squamous cell carcinoma8.39e-0814
cancer1.61e-07235
disease of anatomical entity1.96e-0739
disease of cellular proliferation8.24e-07239


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
CEBPB#105137.971147625824820.001974187055288560.0115689665507396
E2F1#186934.907389214879320.008460985347239390.0327353059450372
EP300#203336.77394172622320.003216880500103790.016826152278777
FOXA1#3169311.08141974938550.000734755275698670.0058368529884151
FOXA2#3170324.63046375266526.68983856509345e-050.00107621695918021
GATA3#2625327.2365163572064.94721007899563e-050.00085430170873053
MYC#460935.22228187160940.007020843755740150.0295820349782445
TFAP2C#7022310.80922860986020.0007916746575753130.00618412188201257



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.