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Coexpression cluster:C2802: Difference between revisions

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|ontology_enrichment_disease=DOID:162!2.95e-23!235;DOID:0050687!2.08e-22!143;DOID:305!2.34e-22!106;DOID:14566!2.76e-22!239;DOID:1749!6.50e-07!14
|ontology_enrichment_disease=DOID:162!2.95e-23!235;DOID:0050687!2.08e-22!143;DOID:305!2.34e-22!106;DOID:14566!2.76e-22!239;DOID:1749!6.50e-07!14
|ontology_enrichment_uberon=UBERON:0004119!1.10e-32!169;UBERON:0000925!1.10e-32!169;UBERON:0006595!1.10e-32!169;UBERON:0001007!3.63e-31!155;UBERON:0001555!3.63e-31!155;UBERON:0007026!3.63e-31!155;UBERON:0004921!7.81e-27!129;UBERON:0004185!7.81e-27!129;UBERON:0000077!3.39e-22!130;UBERON:0001004!7.52e-17!72;UBERON:0000161!1.48e-16!35;UBERON:0003104!1.16e-14!238;UBERON:0009142!1.16e-14!238;UBERON:0001041!1.00e-13!98;UBERON:0001046!4.43e-11!19;UBERON:0000065!5.59e-11!53;UBERON:0005911!7.19e-11!82;UBERON:0000072!1.75e-10!46;UBERON:0008947!4.18e-10!38;UBERON:0003258!4.18e-10!38;UBERON:0000481!1.06e-09!347;UBERON:0000166!2.93e-09!21;UBERON:0000165!6.70e-09!28;UBERON:0000930!6.70e-09!28;UBERON:0000162!7.21e-09!14;UBERON:0001353!7.21e-09!14;UBERON:0000163!7.21e-09!14;UBERON:0006866!7.21e-09!14;UBERON:0000164!7.21e-09!14;UBERON:0000931!7.21e-09!14;UBERON:0005153!9.36e-09!37;UBERON:0002530!6.85e-08!59;UBERON:0003929!7.81e-08!54;UBERON:0004122!8.23e-08!15;UBERON:0000063!9.82e-08!97;UBERON:0003102!1.43e-07!95;UBERON:0005181!1.62e-07!35;UBERON:0000344!2.70e-07!12;UBERON:0005178!3.40e-07!34;UBERON:0002224!3.40e-07!34;UBERON:0002367!3.42e-07!11;UBERON:0010147!3.42e-07!11;UBERON:0009846!3.42e-07!11;UBERON:0003353!3.42e-07!11;UBERON:0004902!3.42e-07!11;UBERON:0003820!3.42e-07!11;UBERON:0009847!3.42e-07!11;UBERON:0000160!4.78e-07!27;UBERON:0005157!6.96e-07!51;UBERON:0000059!7.75e-07!11;UBERON:0005409!8.10e-07!35
|ontology_enrichment_uberon=UBERON:0004119!1.10e-32!169;UBERON:0000925!1.10e-32!169;UBERON:0006595!1.10e-32!169;UBERON:0001007!3.63e-31!155;UBERON:0001555!3.63e-31!155;UBERON:0007026!3.63e-31!155;UBERON:0004921!7.81e-27!129;UBERON:0004185!7.81e-27!129;UBERON:0000077!3.39e-22!130;UBERON:0001004!7.52e-17!72;UBERON:0000161!1.48e-16!35;UBERON:0003104!1.16e-14!238;UBERON:0009142!1.16e-14!238;UBERON:0001041!1.00e-13!98;UBERON:0001046!4.43e-11!19;UBERON:0000065!5.59e-11!53;UBERON:0005911!7.19e-11!82;UBERON:0000072!1.75e-10!46;UBERON:0008947!4.18e-10!38;UBERON:0003258!4.18e-10!38;UBERON:0000481!1.06e-09!347;UBERON:0000166!2.93e-09!21;UBERON:0000165!6.70e-09!28;UBERON:0000930!6.70e-09!28;UBERON:0000162!7.21e-09!14;UBERON:0001353!7.21e-09!14;UBERON:0000163!7.21e-09!14;UBERON:0006866!7.21e-09!14;UBERON:0000164!7.21e-09!14;UBERON:0000931!7.21e-09!14;UBERON:0005153!9.36e-09!37;UBERON:0002530!6.85e-08!59;UBERON:0003929!7.81e-08!54;UBERON:0004122!8.23e-08!15;UBERON:0000063!9.82e-08!97;UBERON:0003102!1.43e-07!95;UBERON:0005181!1.62e-07!35;UBERON:0000344!2.70e-07!12;UBERON:0005178!3.40e-07!34;UBERON:0002224!3.40e-07!34;UBERON:0002367!3.42e-07!11;UBERON:0010147!3.42e-07!11;UBERON:0009846!3.42e-07!11;UBERON:0003353!3.42e-07!11;UBERON:0004902!3.42e-07!11;UBERON:0003820!3.42e-07!11;UBERON:0009847!3.42e-07!11;UBERON:0000160!4.78e-07!27;UBERON:0005157!6.96e-07!51;UBERON:0000059!7.75e-07!11;UBERON:0005409!8.10e-07!35
|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370461473253258!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000632224310213287
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}}
}}

Revision as of 13:19, 5 September 2012


Full id: C2802_esophagus_Prostate_biphenotypic_cervical_tonsil_Smooth_anaplastic



Phase1 CAGE Peaks

Hg19::chr5:134364600..134364638,-p@chr5:134364600..134364638
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Hg19::chr5:134364906..134364931,-p@chr5:134364906..134364931
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Hg19::chr5:134364965..134364981,-p@chr5:134364965..134364981
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Hg19::chr5:134369879..134369898,-p2@PITX1


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 cell5.57e-16254
endo-epithelial cell3.58e-1543
endodermal cell4.20e-1559
epithelial cell of alimentary canal5.09e-1021
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.10e-32169
endoderm1.10e-32169
presumptive endoderm1.10e-32169
digestive system3.63e-31155
digestive tract3.63e-31155
primitive gut3.63e-31155
subdivision of digestive tract7.81e-27129
endodermal part of digestive tract7.81e-27129
mixed endoderm/mesoderm-derived structure3.39e-22130
respiratory system7.52e-1772
orifice1.48e-1635
mesenchyme1.16e-14238
entire embryonic mesenchyme1.16e-14238
foregut1.00e-1398
hindgut4.43e-1119
respiratory tract5.59e-1153
endo-epithelium7.19e-1182
segment of respiratory tract1.75e-1046
respiratory primordium4.18e-1038
endoderm of foregut4.18e-1038
multi-tissue structure1.06e-09347
oral opening2.93e-0921
mouth6.70e-0928
stomodeum6.70e-0928
cloaca7.21e-0914
anal region7.21e-0914
embryonic cloaca7.21e-0914
terminal part of digestive tract7.21e-0914
primitive urogenital sinus7.21e-0914
proctodeum7.21e-0914
epithelial bud9.36e-0937
gland6.85e-0859
gut epithelium7.81e-0854
genitourinary system8.23e-0815
organ segment9.82e-0897
surface structure1.43e-0795
thoracic segment organ1.62e-0735
mucosa2.70e-0712
thoracic cavity element3.40e-0734
thoracic cavity3.40e-0734
prostate gland3.42e-0711
male accessory sex gland3.42e-0711
embryonic cloacal epithelium3.42e-0711
epithelium of hindgut3.42e-0711
urogenital sinus epithelium3.42e-0711
prostate bud3.42e-0711
prostate field3.42e-0711
intestine4.78e-0727
epithelial fold6.96e-0751
large intestine7.75e-0711
gastrointestinal system8.10e-0735
Disease
Ontology termp-valuen
cancer2.95e-23235
cell type cancer2.08e-22143
carcinoma2.34e-22106
disease of cellular proliferation2.76e-22239
squamous cell carcinoma6.50e-0714


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
CTBP2#1488347.03775025449611.60047699357395e-050.000370461473253258
SUZ12#23512337.58683568329723.12785741999833e-050.000632224310213287



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.