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Coexpression cluster:C4107: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.51e-35!106;DOID:0050687!1.70e-28!143;DOID:162!4.72e-18!235;DOID:14566!7.37e-17!239;DOID:299!3.30e-13!25;DOID:1749!9.24e-12!14
|ontology_enrichment_disease=DOID:305!1.51e-35!106;DOID:0050687!1.70e-28!143;DOID:162!4.72e-18!235;DOID:14566!7.37e-17!239;DOID:299!3.30e-13!25;DOID:1749!9.24e-12!14
|ontology_enrichment_uberon=UBERON:0000065!6.00e-19!53;UBERON:0001004!7.04e-18!72;UBERON:0004119!1.00e-17!169;UBERON:0000925!1.00e-17!169;UBERON:0006595!1.00e-17!169;UBERON:0008947!1.35e-17!38;UBERON:0003258!1.35e-17!38;UBERON:0000072!3.47e-15!46;UBERON:0001007!9.91e-15!155;UBERON:0001555!9.91e-15!155;UBERON:0007026!9.91e-15!155;UBERON:0000064!4.09e-13!219;UBERON:0005177!2.79e-12!107;UBERON:0000077!7.82e-12!130;UBERON:0000062!1.69e-11!511;UBERON:0004921!2.36e-11!129;UBERON:0004185!2.36e-11!129;UBERON:0001041!3.35e-11!98;UBERON:0005178!7.57e-11!34;UBERON:0002224!7.57e-11!34;UBERON:0000058!8.46e-11!26;UBERON:0005911!1.30e-10!82;UBERON:0000464!1.68e-10!104;UBERON:0001008!2.14e-10!45;UBERON:0005181!2.93e-10!35;UBERON:0006554!6.58e-10!44;UBERON:0000481!9.69e-10!347;UBERON:0000489!5.27e-09!32;UBERON:0002048!5.49e-09!22;UBERON:0000117!5.49e-09!22;UBERON:0000171!5.49e-09!22;UBERON:0000170!5.49e-09!22;UBERON:0005597!5.49e-09!22;UBERON:0000118!5.49e-09!22;UBERON:0000466!8.15e-09!126;UBERON:0000475!1.06e-08!365;UBERON:0003064!1.40e-08!37;UBERON:0009569!2.08e-08!113;UBERON:0005153!3.07e-08!37;UBERON:0001737!5.43e-08!9;UBERON:0002113!6.32e-08!27;UBERON:0003918!6.32e-08!27;UBERON:0005095!6.32e-08!27;UBERON:0007687!6.32e-08!27;UBERON:0004802!1.19e-07!19;UBERON:0000115!1.19e-07!19;UBERON:0004807!1.43e-07!28;UBERON:0000080!1.51e-07!18;UBERON:0002120!1.51e-07!18;UBERON:0004875!1.51e-07!18;UBERON:0005721!1.51e-07!18;UBERON:0005754!1.51e-07!18;UBERON:0007297!1.51e-07!18;UBERON:0009773!2.18e-07!12;UBERON:0001231!2.18e-07!12;UBERON:0004810!2.18e-07!12;UBERON:0006555!3.39e-07!17;UBERON:0005103!3.39e-07!17;UBERON:0000083!3.39e-07!17;UBERON:0009201!3.39e-07!17;UBERON:0004819!3.39e-07!17;UBERON:0006553!3.39e-07!17;UBERON:0003074!3.39e-07!17;UBERON:0003060!3.39e-07!17;UBERON:0004876!3.90e-07!20;UBERON:0001557!4.68e-07!19;UBERON:0007196!5.89e-07!14;UBERON:0001558!5.89e-07!14;UBERON:0000915!6.82e-07!52;UBERON:0004211!8.32e-07!16;UBERON:0001285!8.32e-07!16;UBERON:0007684!8.32e-07!16;UBERON:0003220!8.32e-07!16;UBERON:0004208!8.32e-07!16;UBERON:0000344!9.35e-07!12
|ontology_enrichment_uberon=UBERON:0000065!6.00e-19!53;UBERON:0001004!7.04e-18!72;UBERON:0004119!1.00e-17!169;UBERON:0000925!1.00e-17!169;UBERON:0006595!1.00e-17!169;UBERON:0008947!1.35e-17!38;UBERON:0003258!1.35e-17!38;UBERON:0000072!3.47e-15!46;UBERON:0001007!9.91e-15!155;UBERON:0001555!9.91e-15!155;UBERON:0007026!9.91e-15!155;UBERON:0000064!4.09e-13!219;UBERON:0005177!2.79e-12!107;UBERON:0000077!7.82e-12!130;UBERON:0000062!1.69e-11!511;UBERON:0004921!2.36e-11!129;UBERON:0004185!2.36e-11!129;UBERON:0001041!3.35e-11!98;UBERON:0005178!7.57e-11!34;UBERON:0002224!7.57e-11!34;UBERON:0000058!8.46e-11!26;UBERON:0005911!1.30e-10!82;UBERON:0000464!1.68e-10!104;UBERON:0001008!2.14e-10!45;UBERON:0005181!2.93e-10!35;UBERON:0006554!6.58e-10!44;UBERON:0000481!9.69e-10!347;UBERON:0000489!5.27e-09!32;UBERON:0002048!5.49e-09!22;UBERON:0000117!5.49e-09!22;UBERON:0000171!5.49e-09!22;UBERON:0000170!5.49e-09!22;UBERON:0005597!5.49e-09!22;UBERON:0000118!5.49e-09!22;UBERON:0000466!8.15e-09!126;UBERON:0000475!1.06e-08!365;UBERON:0003064!1.40e-08!37;UBERON:0009569!2.08e-08!113;UBERON:0005153!3.07e-08!37;UBERON:0001737!5.43e-08!9;UBERON:0002113!6.32e-08!27;UBERON:0003918!6.32e-08!27;UBERON:0005095!6.32e-08!27;UBERON:0007687!6.32e-08!27;UBERON:0004802!1.19e-07!19;UBERON:0000115!1.19e-07!19;UBERON:0004807!1.43e-07!28;UBERON:0000080!1.51e-07!18;UBERON:0002120!1.51e-07!18;UBERON:0004875!1.51e-07!18;UBERON:0005721!1.51e-07!18;UBERON:0005754!1.51e-07!18;UBERON:0007297!1.51e-07!18;UBERON:0009773!2.18e-07!12;UBERON:0001231!2.18e-07!12;UBERON:0004810!2.18e-07!12;UBERON:0006555!3.39e-07!17;UBERON:0005103!3.39e-07!17;UBERON:0000083!3.39e-07!17;UBERON:0009201!3.39e-07!17;UBERON:0004819!3.39e-07!17;UBERON:0006553!3.39e-07!17;UBERON:0003074!3.39e-07!17;UBERON:0003060!3.39e-07!17;UBERON:0004876!3.90e-07!20;UBERON:0001557!4.68e-07!19;UBERON:0007196!5.89e-07!14;UBERON:0001558!5.89e-07!14;UBERON:0000915!6.82e-07!52;UBERON:0004211!8.32e-07!16;UBERON:0001285!8.32e-07!16;UBERON:0007684!8.32e-07!16;UBERON:0003220!8.32e-07!16;UBERON:0004208!8.32e-07!16;UBERON:0000344!9.35e-07!12
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}}
}}

Revision as of 12:55, 5 September 2012


Full id: C4107_Renal_pharyngeal_oral_cervical_tubular_keratoacanthoma_bronchial



Phase1 CAGE Peaks

Hg19::chr22:46373004..46373016,-p3@WNT7B
Hg19::chr22:46373034..46373058,-p1@WNT7B
Hg19::chr22:46373131..46373140,-p4@WNT7B


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
respiratory tract6.00e-1953
respiratory system7.04e-1872
endoderm-derived structure1.00e-17169
endoderm1.00e-17169
presumptive endoderm1.00e-17169
respiratory primordium1.35e-1738
endoderm of foregut1.35e-1738
segment of respiratory tract3.47e-1546
digestive system9.91e-15155
digestive tract9.91e-15155
primitive gut9.91e-15155
organ part4.09e-13219
trunk region element2.79e-12107
mixed endoderm/mesoderm-derived structure7.82e-12130
organ1.69e-11511
subdivision of digestive tract2.36e-11129
endodermal part of digestive tract2.36e-11129
foregut3.35e-1198
thoracic cavity element7.57e-1134
thoracic cavity7.57e-1134
duct8.46e-1126
endo-epithelium1.30e-1082
anatomical space1.68e-10104
renal system2.14e-1045
thoracic segment organ2.93e-1035
urinary system structure6.58e-1044
multi-tissue structure9.69e-10347
cavitated compound organ5.27e-0932
lung5.49e-0922
respiratory tube5.49e-0922
respiration organ5.49e-0922
pair of lungs5.49e-0922
lung primordium5.49e-0922
lung bud5.49e-0922
immaterial anatomical entity8.15e-09126
organism subdivision1.06e-08365
intermediate mesoderm1.40e-0837
subdivision of trunk2.08e-08113
epithelial bud3.07e-0837
larynx5.43e-089
kidney6.32e-0827
kidney mesenchyme6.32e-0827
kidney rudiment6.32e-0827
kidney field6.32e-0827
respiratory tract epithelium1.19e-0719
lung epithelium1.19e-0719
respiratory system epithelium1.43e-0728
mesonephros1.51e-0718
pronephros1.51e-0718
nephrogenic cord1.51e-0718
pronephric mesoderm1.51e-0718
rostral part of nephrogenic cord1.51e-0718
presumptive pronephric mesoderm1.51e-0718
renal tubule2.18e-0712
nephron tubule2.18e-0712
nephron tubule epithelium2.18e-0712
excretory tube3.39e-0717
mesonephric epithelium3.39e-0717
mesonephric tubule3.39e-0717
nephric duct3.39e-0717
kidney epithelium3.39e-0717
renal duct3.39e-0717
mesonephric duct3.39e-0717
pronephric duct3.39e-0717
urogenital ridge3.90e-0720
upper respiratory tract4.68e-0719
tracheobronchial tree5.89e-0714
lower respiratory tract5.89e-0714
thoracic segment of trunk6.82e-0752
nephron epithelium8.32e-0716
nephron8.32e-0716
uriniferous tubule8.32e-0716
metanephric mesenchyme8.32e-0716
nephrogenic mesenchyme8.32e-0716
mucosa9.35e-0712
Disease
Ontology termp-valuen
carcinoma1.51e-35106
cell type cancer1.70e-28143
cancer4.72e-18235
disease of cellular proliferation7.37e-17239
adenocarcinoma3.30e-1325
squamous cell carcinoma9.24e-1214


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)

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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
E2F1#186934.907389214879320.008460985347239390.0326024516189616
TFAP2C#7022310.80922860986020.0007916746575753130.00616797534968356



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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