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Coexpression cluster:C2862: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.90e-19!106;DOID:1749!1.78e-16!14;DOID:299!5.77e-14!25;DOID:0050687!5.21e-10!143
|ontology_enrichment_disease=DOID:305!4.90e-19!106;DOID:1749!1.78e-16!14;DOID:299!5.77e-14!25;DOID:0050687!5.21e-10!143
|ontology_enrichment_uberon=UBERON:0004119!6.95e-28!169;UBERON:0000925!6.95e-28!169;UBERON:0006595!6.95e-28!169;UBERON:0001007!1.17e-22!155;UBERON:0001555!1.17e-22!155;UBERON:0007026!1.17e-22!155;UBERON:0001004!2.04e-19!72;UBERON:0000464!4.14e-18!104;UBERON:0000466!1.57e-15!126;UBERON:0005911!1.68e-15!82;UBERON:0004921!1.94e-15!129;UBERON:0004185!1.94e-15!129;UBERON:0000077!8.15e-15!130;UBERON:0000161!4.38e-14!35;UBERON:0000065!3.38e-13!53;UBERON:0005153!3.52e-13!37;UBERON:0005181!6.88e-13!35;UBERON:0005178!2.76e-12!34;UBERON:0002224!2.76e-12!34;UBERON:0000062!3.87e-12!511;UBERON:0001008!8.29e-12!45;UBERON:0005177!2.22e-11!107;UBERON:0001041!2.90e-11!98;UBERON:0006554!4.88e-11!44;UBERON:0000166!6.00e-11!21;UBERON:0005157!3.65e-10!51;UBERON:0005156!9.64e-10!59;UBERON:0000990!9.64e-10!59;UBERON:0002048!4.56e-09!22;UBERON:0000117!4.56e-09!22;UBERON:0000171!4.56e-09!22;UBERON:0000170!4.56e-09!22;UBERON:0005597!4.56e-09!22;UBERON:0000118!4.56e-09!22;UBERON:0008947!7.23e-09!38;UBERON:0003258!7.23e-09!38;UBERON:0003104!8.39e-09!238;UBERON:0009142!8.39e-09!238;UBERON:0000072!9.29e-09!46;UBERON:0003100!1.00e-08!41;UBERON:0000058!1.09e-08!26;UBERON:0000915!1.16e-08!52;UBERON:0004807!1.72e-08!28;UBERON:0000467!1.75e-08!625;UBERON:0003133!1.85e-08!48;UBERON:0000480!2.08e-08!626;UBERON:0003064!2.42e-08!37;UBERON:0009569!2.44e-08!113;UBERON:0000165!2.97e-08!28;UBERON:0000930!2.97e-08!28;UBERON:0002553!4.40e-08!70;UBERON:0000481!6.13e-08!347;UBERON:0007196!8.17e-08!14;UBERON:0001558!8.17e-08!14;UBERON:0000922!1.51e-07!612;UBERON:0004175!1.55e-07!25;UBERON:0000344!2.52e-07!12;UBERON:0000923!2.87e-07!604;UBERON:0005291!2.87e-07!604;UBERON:0006598!2.87e-07!604;UBERON:0002532!2.87e-07!604;UBERON:0002050!3.38e-07!605;UBERON:0005423!3.38e-07!605;UBERON:0002294!4.33e-07!7;UBERON:0001173!4.33e-07!7;UBERON:0004912!4.33e-07!7;UBERON:0000468!5.85e-07!659;UBERON:0009773!6.24e-07!12;UBERON:0001231!6.24e-07!12;UBERON:0004810!6.24e-07!12;UBERON:0000489!6.29e-07!32;UBERON:0004802!7.48e-07!19;UBERON:0000115!7.48e-07!19;UBERON:0003102!7.57e-07!95
|ontology_enrichment_uberon=UBERON:0004119!6.95e-28!169;UBERON:0000925!6.95e-28!169;UBERON:0006595!6.95e-28!169;UBERON:0001007!1.17e-22!155;UBERON:0001555!1.17e-22!155;UBERON:0007026!1.17e-22!155;UBERON:0001004!2.04e-19!72;UBERON:0000464!4.14e-18!104;UBERON:0000466!1.57e-15!126;UBERON:0005911!1.68e-15!82;UBERON:0004921!1.94e-15!129;UBERON:0004185!1.94e-15!129;UBERON:0000077!8.15e-15!130;UBERON:0000161!4.38e-14!35;UBERON:0000065!3.38e-13!53;UBERON:0005153!3.52e-13!37;UBERON:0005181!6.88e-13!35;UBERON:0005178!2.76e-12!34;UBERON:0002224!2.76e-12!34;UBERON:0000062!3.87e-12!511;UBERON:0001008!8.29e-12!45;UBERON:0005177!2.22e-11!107;UBERON:0001041!2.90e-11!98;UBERON:0006554!4.88e-11!44;UBERON:0000166!6.00e-11!21;UBERON:0005157!3.65e-10!51;UBERON:0005156!9.64e-10!59;UBERON:0000990!9.64e-10!59;UBERON:0002048!4.56e-09!22;UBERON:0000117!4.56e-09!22;UBERON:0000171!4.56e-09!22;UBERON:0000170!4.56e-09!22;UBERON:0005597!4.56e-09!22;UBERON:0000118!4.56e-09!22;UBERON:0008947!7.23e-09!38;UBERON:0003258!7.23e-09!38;UBERON:0003104!8.39e-09!238;UBERON:0009142!8.39e-09!238;UBERON:0000072!9.29e-09!46;UBERON:0003100!1.00e-08!41;UBERON:0000058!1.09e-08!26;UBERON:0000915!1.16e-08!52;UBERON:0004807!1.72e-08!28;UBERON:0000467!1.75e-08!625;UBERON:0003133!1.85e-08!48;UBERON:0000480!2.08e-08!626;UBERON:0003064!2.42e-08!37;UBERON:0009569!2.44e-08!113;UBERON:0000165!2.97e-08!28;UBERON:0000930!2.97e-08!28;UBERON:0002553!4.40e-08!70;UBERON:0000481!6.13e-08!347;UBERON:0007196!8.17e-08!14;UBERON:0001558!8.17e-08!14;UBERON:0000922!1.51e-07!612;UBERON:0004175!1.55e-07!25;UBERON:0000344!2.52e-07!12;UBERON:0000923!2.87e-07!604;UBERON:0005291!2.87e-07!604;UBERON:0006598!2.87e-07!604;UBERON:0002532!2.87e-07!604;UBERON:0002050!3.38e-07!605;UBERON:0005423!3.38e-07!605;UBERON:0002294!4.33e-07!7;UBERON:0001173!4.33e-07!7;UBERON:0004912!4.33e-07!7;UBERON:0000468!5.85e-07!659;UBERON:0009773!6.24e-07!12;UBERON:0001231!6.24e-07!12;UBERON:0004810!6.24e-07!12;UBERON:0000489!6.29e-07!32;UBERON:0004802!7.48e-07!19;UBERON:0000115!7.48e-07!19;UBERON:0003102!7.57e-07!95
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}}
}}

Revision as of 13:13, 5 September 2012


Full id: C2862_lung_bronchioalveolar_epidermoid_prostate_mucinous_bile_squamous



Phase1 CAGE Peaks

Hg19::chr6:47009992..47009993,-p4@GPR110
Hg19::chr6:47009996..47010035,-p2@GPR110
Hg19::chr6:47010042..47010053,-p3@GPR110
Hg19::chr6:47010061..47010104,-p1@GPR110


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
endoderm-derived structure6.95e-28169
endoderm6.95e-28169
presumptive endoderm6.95e-28169
digestive system1.17e-22155
digestive tract1.17e-22155
primitive gut1.17e-22155
respiratory system2.04e-1972
anatomical space4.14e-18104
immaterial anatomical entity1.57e-15126
endo-epithelium1.68e-1582
subdivision of digestive tract1.94e-15129
endodermal part of digestive tract1.94e-15129
mixed endoderm/mesoderm-derived structure8.15e-15130
orifice4.38e-1435
respiratory tract3.38e-1353
epithelial bud3.52e-1337
thoracic segment organ6.88e-1335
thoracic cavity element2.76e-1234
thoracic cavity2.76e-1234
organ3.87e-12511
renal system8.29e-1245
trunk region element2.22e-11107
foregut2.90e-1198
urinary system structure4.88e-1144
oral opening6.00e-1121
epithelial fold3.65e-1051
reproductive structure9.64e-1059
reproductive system9.64e-1059
lung4.56e-0922
respiratory tube4.56e-0922
respiration organ4.56e-0922
pair of lungs4.56e-0922
lung primordium4.56e-0922
lung bud4.56e-0922
respiratory primordium7.23e-0938
endoderm of foregut7.23e-0938
mesenchyme8.39e-09238
entire embryonic mesenchyme8.39e-09238
segment of respiratory tract9.29e-0946
female organism1.00e-0841
duct1.09e-0826
thoracic segment of trunk1.16e-0852
respiratory system epithelium1.72e-0828
anatomical system1.75e-08625
reproductive organ1.85e-0848
anatomical group2.08e-08626
intermediate mesoderm2.42e-0837
subdivision of trunk2.44e-08113
mouth2.97e-0828
stomodeum2.97e-0828
anatomical cavity4.40e-0870
multi-tissue structure6.13e-08347
tracheobronchial tree8.17e-0814
lower respiratory tract8.17e-0814
embryo1.51e-07612
internal genitalia1.55e-0725
mucosa2.52e-0712
germ layer2.87e-07604
embryonic tissue2.87e-07604
presumptive structure2.87e-07604
epiblast (generic)2.87e-07604
embryonic structure3.38e-07605
developing anatomical structure3.38e-07605
biliary system4.33e-077
biliary tree4.33e-077
biliary bud4.33e-077
multi-cellular organism5.85e-07659
renal tubule6.24e-0712
nephron tubule6.24e-0712
nephron tubule epithelium6.24e-0712
cavitated compound organ6.29e-0732
respiratory tract epithelium7.48e-0719
lung epithelium7.48e-0719
surface structure7.57e-0795
Disease
Ontology termp-valuen
carcinoma4.90e-19106
squamous cell carcinoma1.78e-1614
adenocarcinoma5.77e-1425
cell type cancer5.21e-10143


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
ESR1#2099430.76860329615451.11467714392546e-064.6160097634588e-05
GATA3#2625427.2365163572061.81561517799785e-066.79158429709588e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444459201067435
STAT3#6774410.51946499715428.16377768286615e-050.00123496056984481



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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