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Coexpression cluster:C4107: Difference between revisions

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|full_id=C4107_Renal_pharyngeal_oral_cervical_tubular_keratoacanthoma_bronchial
|full_id=C4107_Renal_pharyngeal_oral_cervical_tubular_keratoacanthoma_bronchial
|id=C4107
|id=C4107
|ontology_enrichment_celltype=CL:0000066!3.62e-40!254;CL:0002076!2.40e-19!43;CL:0000223!5.32e-16!59;CL:0002368!5.25e-10!13;CL:0002251!1.84e-08!21;CL:0000082!1.19e-07!19;CL:0002202!1.71e-07!9;CL:0002632!1.71e-07!9;CL:1000507!2.18e-07!12;CL:1000494!2.18e-07!12;CL:0000076!4.13e-07!62;CL:1000449!8.32e-07!16
|ontology_enrichment_celltype=CL:0000066!8.01e-44!253;CL:0002076!5.64e-20!42;CL:0000223!3.19e-15!58;CL:0002368!4.45e-13!13;CL:1000507!4.81e-12!10;CL:1000494!4.81e-12!10;CL:0002202!1.36e-09!9;CL:0002632!1.36e-09!9;CL:1000497!7.99e-09!17;CL:0002518!7.99e-09!17;CL:1000449!9.62e-09!15;CL:0000082!1.74e-08!19;CL:0000076!3.38e-07!63;CL:0002251!8.30e-07!20
|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!6.15e-40!106;DOID:0050687!1.07e-28!143;DOID:162!5.61e-18!235;DOID:14566!4.94e-17!239;DOID:1749!1.90e-14!14;DOID:299!5.64e-13!25
|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!8.39e-21!54;UBERON:0001004!1.11e-19!74;UBERON:0004119!3.92e-19!160;UBERON:0000925!3.92e-19!160;UBERON:0006595!3.92e-19!160;UBERON:0008947!7.72e-19!38;UBERON:0003258!7.72e-19!38;UBERON:0000072!4.06e-17!47;UBERON:0001007!1.45e-15!145;UBERON:0001555!1.45e-15!145;UBERON:0007026!1.45e-15!145;UBERON:0005177!3.00e-13!101;UBERON:0004810!4.81e-12!10;UBERON:0001041!1.28e-11!87;UBERON:0005178!1.30e-11!34;UBERON:0002224!1.30e-11!34;UBERON:0001008!1.81e-11!48;UBERON:0004921!1.94e-11!118;UBERON:0005181!4.43e-11!35;UBERON:0006554!6.71e-11!47;UBERON:0000064!7.49e-11!218;UBERON:0005911!1.84e-10!82;UBERON:0009569!9.05e-10!112;UBERON:0005153!1.23e-09!37;UBERON:0001737!1.97e-09!9;UBERON:0002048!5.42e-09!22;UBERON:0000117!5.42e-09!22;UBERON:0000171!5.42e-09!22;UBERON:0000170!5.42e-09!22;UBERON:0005597!5.42e-09!22;UBERON:0000118!5.42e-09!22;UBERON:0000489!7.37e-09!31;UBERON:0004211!9.62e-09!15;UBERON:0009773!9.62e-09!15;UBERON:0001231!9.62e-09!15;UBERON:0001285!9.62e-09!15;UBERON:0007684!9.62e-09!15;UBERON:0004208!9.62e-09!15;UBERON:0000915!1.19e-08!52;UBERON:0004807!1.25e-08!28;UBERON:0001557!1.50e-08!19;UBERON:0004802!1.74e-08!19;UBERON:0000115!1.74e-08!19;UBERON:0000475!2.76e-08!264;UBERON:0002113!5.21e-08!26;UBERON:0003918!5.21e-08!26;UBERON:0011143!5.21e-08!26;UBERON:0005095!5.21e-08!26;UBERON:0007687!5.21e-08!26;UBERON:0006555!5.45e-08!16;UBERON:0004819!5.45e-08!16;UBERON:0000464!6.80e-08!95;UBERON:0005157!7.12e-08!47;UBERON:0007196!2.39e-07!15;UBERON:0001558!2.39e-07!15;UBERON:0000161!5.49e-07!36;UBERON:0000481!5.75e-07!342;UBERON:0000062!7.69e-07!503
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326024516189616!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616797534968356
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326024516189616!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616797534968356
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}}
}}

Revision as of 15:41, 19 October 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 tract8.39e-2154
respiratory system1.11e-1974
endoderm-derived structure3.92e-19160
endoderm3.92e-19160
presumptive endoderm3.92e-19160
respiratory primordium7.72e-1938
endoderm of foregut7.72e-1938
segment of respiratory tract4.06e-1747
digestive system1.45e-15145
digestive tract1.45e-15145
primitive gut1.45e-15145
trunk region element3.00e-13101
nephron tubule epithelium4.81e-1210
foregut1.28e-1187
thoracic cavity element1.30e-1134
thoracic cavity1.30e-1134
renal system1.81e-1148
subdivision of digestive tract1.94e-11118
thoracic segment organ4.43e-1135
urinary system structure6.71e-1147
organ part7.49e-11218
endo-epithelium1.84e-1082
subdivision of trunk9.05e-10112
epithelial bud1.23e-0937
larynx1.97e-099
lung5.42e-0922
respiratory tube5.42e-0922
respiration organ5.42e-0922
pair of lungs5.42e-0922
lung primordium5.42e-0922
lung bud5.42e-0922
cavitated compound organ7.37e-0931
nephron epithelium9.62e-0915
renal tubule9.62e-0915
nephron tubule9.62e-0915
nephron9.62e-0915
uriniferous tubule9.62e-0915
nephrogenic mesenchyme9.62e-0915
thoracic segment of trunk1.19e-0852
respiratory system epithelium1.25e-0828
upper respiratory tract1.50e-0819
respiratory tract epithelium1.74e-0819
lung epithelium1.74e-0819
organism subdivision2.76e-08264
kidney5.21e-0826
kidney mesenchyme5.21e-0826
upper urinary tract5.21e-0826
kidney rudiment5.21e-0826
kidney field5.21e-0826
excretory tube5.45e-0816
kidney epithelium5.45e-0816
anatomical space6.80e-0895
epithelial fold7.12e-0847
tracheobronchial tree2.39e-0715
lower respiratory tract2.39e-0715
orifice5.49e-0736
multi-tissue structure5.75e-07342
organ7.69e-07503
Disease
Ontology termp-valuen
carcinoma6.15e-40106
cell type cancer1.07e-28143
cancer5.61e-18235
disease of cellular proliferation4.94e-17239
squamous cell carcinoma1.90e-1414
adenocarcinoma5.64e-1325


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
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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