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Coexpression cluster:C2064: Difference between revisions

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|ontology_enrichment_disease=DOID:5093!4.09e-21!4;DOID:1612!4.09e-21!4;DOID:7!1.14e-15!39;DOID:305!1.30e-15!106;DOID:0050687!1.66e-14!143;DOID:162!2.25e-08!235;DOID:14566!4.38e-08!239;DOID:299!9.03e-07!25
|ontology_enrichment_disease=DOID:5093!4.09e-21!4;DOID:1612!4.09e-21!4;DOID:7!1.14e-15!39;DOID:305!1.30e-15!106;DOID:0050687!1.66e-14!143;DOID:162!2.25e-08!235;DOID:14566!4.38e-08!239;DOID:299!9.03e-07!25
|ontology_enrichment_uberon=UBERON:0000476!8.57e-16!3;UBERON:0000920!8.57e-16!3;UBERON:0003124!7.81e-12!7;UBERON:0005911!9.23e-12!82;UBERON:0003929!5.69e-09!54;UBERON:0005631!8.90e-09!14;UBERON:0000158!8.90e-09!14;UBERON:0009497!1.08e-08!25;UBERON:0000015!1.08e-08!25;UBERON:0002423!1.08e-08!25;UBERON:0006235!1.08e-08!25;UBERON:0004161!1.08e-08!25;UBERON:0007499!1.18e-08!25;UBERON:0000310!1.70e-08!10;UBERON:0009856!2.74e-08!26;UBERON:0001443!1.00e-07!11;UBERON:0008835!1.97e-07!22;UBERON:0003894!1.97e-07!22;UBERON:0005153!2.96e-07!37;UBERON:0000077!3.57e-07!130;UBERON:0004921!3.66e-07!129;UBERON:0004185!3.66e-07!129;UBERON:0001007!4.29e-07!155;UBERON:0001555!4.29e-07!155;UBERON:0007026!4.29e-07!155;UBERON:0009854!4.39e-07!23;UBERON:0004119!4.45e-07!169;UBERON:0000925!4.45e-07!169;UBERON:0006595!4.45e-07!169
|ontology_enrichment_uberon=UBERON:0000476!8.57e-16!3;UBERON:0000920!8.57e-16!3;UBERON:0003124!7.81e-12!7;UBERON:0005911!9.23e-12!82;UBERON:0003929!5.69e-09!54;UBERON:0005631!8.90e-09!14;UBERON:0000158!8.90e-09!14;UBERON:0009497!1.08e-08!25;UBERON:0000015!1.08e-08!25;UBERON:0002423!1.08e-08!25;UBERON:0006235!1.08e-08!25;UBERON:0004161!1.08e-08!25;UBERON:0007499!1.18e-08!25;UBERON:0000310!1.70e-08!10;UBERON:0009856!2.74e-08!26;UBERON:0001443!1.00e-07!11;UBERON:0008835!1.97e-07!22;UBERON:0003894!1.97e-07!22;UBERON:0005153!2.96e-07!37;UBERON:0000077!3.57e-07!130;UBERON:0004921!3.66e-07!129;UBERON:0004185!3.66e-07!129;UBERON:0001007!4.29e-07!155;UBERON:0001555!4.29e-07!155;UBERON:0007026!4.29e-07!155;UBERON:0009854!4.39e-07!23;UBERON:0004119!4.45e-07!169;UBERON:0000925!4.45e-07!169;UBERON:0006595!4.45e-07!169
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267429692195655!EP300#2033;4:6.7739417262232:0.000474845982144264:0.0043338669517753!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175697000853357!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00106896883090952!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.41421636582406e-05!GATA3#2625;3:20.4273872679045:0.000192441557625832:0.00231842240591582!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000625559710791993!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.65601148314664e-05!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00682908491833827!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.0011516026398778
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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C2064_Intestinal_choriocarcinoma_breast_Prostate_pancreatic_colon_MCF7



Phase1 CAGE Peaks

Hg19::chr10:5535609..5535633,-p@chr10:5535609..5535633
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Hg19::chr10:5535635..5535648,-p@chr10:5535635..5535648
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Hg19::chr10:5535762..5535773,-p@chr10:5535762..5535773
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Hg19::chr6:3789350..3789355,-p@chr6:3789350..3789355
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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
chorionic membrane mesenchymal stem cell8.57e-163
germ line cell6.79e-127
germ cell6.79e-127
endodermal cell1.13e-0959
metabolising cell9.95e-0712
endopolyploid cell9.95e-0712
parenchymal cell9.95e-0712
polyploid cell9.95e-0712
hepatocyte9.95e-0712
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure8.57e-163
egg chorion8.57e-163
chorion7.81e-127
endo-epithelium9.23e-1282
gut epithelium5.69e-0954
extraembryonic membrane8.90e-0914
membranous layer8.90e-0914
epithelium of foregut-midgut junction1.08e-0825
anatomical boundary1.08e-0825
hepatobiliary system1.08e-0825
foregut-midgut junction1.08e-0825
septum transversum1.08e-0825
epithelial sac1.18e-0825
breast1.70e-0810
sac2.74e-0826
chest1.00e-0711
hepatic diverticulum1.97e-0722
liver primordium1.97e-0722
epithelial bud2.96e-0737
mixed endoderm/mesoderm-derived structure3.57e-07130
subdivision of digestive tract3.66e-07129
endodermal part of digestive tract3.66e-07129
digestive system4.29e-07155
digestive tract4.29e-07155
primitive gut4.29e-07155
digestive tract diverticulum4.39e-0723
endoderm-derived structure4.45e-07169
endoderm4.45e-07169
presumptive endoderm4.45e-07169
Disease
Ontology termp-valuen
thoracic cancer4.09e-214
breast cancer4.09e-214
disease of anatomical entity1.14e-1539
carcinoma1.30e-15106
cell type cancer1.66e-14143
cancer2.25e-08235
disease of cellular proliferation4.38e-08239
adenocarcinoma9.03e-0725


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#105147.971147625824820.0002476385788090830.00267429692195655
EP300#203346.77394172622320.0004748459821442640.0043338669517753
ESR1#2099323.07645247211590.0001339105244968570.00175697000853357
FOXA1#3169411.08141974938556.62943068949433e-050.00106896883090952
FOXA2#3170424.63046375266522.71504128667089e-069.41421636582406e-05
GATA3#2625320.42738726790450.0001924415576258320.00231842240591582
HDAC2#3066413.41562023662633.0859005065161e-050.000625559710791993
HNF4G#3174428.75342252644681.46167379934821e-065.65601148314664e-05
SP1#666745.69838137814090.0009482606065333980.00682908491833827
TCF7L2#6934410.77017656313737.42969445082454e-050.0011516026398778



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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