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Coexpression cluster:C4617: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.04e-24!106;DOID:0050687!1.26e-17!143;DOID:299!2.93e-10!25;DOID:1749!3.69e-10!14;DOID:162!7.87e-07!235;DOID:14566!8.60e-07!239
|ontology_enrichment_disease=DOID:305!3.04e-24!106;DOID:0050687!1.26e-17!143;DOID:299!2.93e-10!25;DOID:1749!3.69e-10!14;DOID:162!7.87e-07!235;DOID:14566!8.60e-07!239
|ontology_enrichment_uberon=UBERON:0004119!9.02e-29!169;UBERON:0000925!9.02e-29!169;UBERON:0006595!9.02e-29!169;UBERON:0001007!1.52e-23!155;UBERON:0001555!1.52e-23!155;UBERON:0007026!1.52e-23!155;UBERON:0004921!2.44e-20!129;UBERON:0004185!2.44e-20!129;UBERON:0000077!3.15e-17!130;UBERON:0001004!1.56e-16!72;UBERON:0001041!2.46e-13!98;UBERON:0000065!2.46e-13!53;UBERON:0000062!2.20e-11!511;UBERON:0005911!1.76e-10!82;UBERON:0000464!2.13e-10!104;UBERON:0000072!4.50e-10!46;UBERON:0008947!1.16e-09!38;UBERON:0003258!1.16e-09!38;UBERON:0001048!2.03e-09!168;UBERON:0000466!3.30e-09!126;UBERON:0000161!5.25e-09!35;UBERON:0000922!8.15e-09!612;UBERON:0000481!1.27e-08!347;UBERON:0000468!1.62e-08!659;UBERON:0003104!2.44e-08!238;UBERON:0009142!2.44e-08!238;UBERON:0000344!3.70e-08!12;UBERON:0000160!3.89e-08!27;UBERON:0000064!4.10e-08!219;UBERON:0005409!7.18e-08!35;UBERON:0000166!9.76e-08!21;UBERON:0005177!2.87e-07!107;UBERON:0002050!3.65e-07!605;UBERON:0005423!3.65e-07!605;UBERON:0005153!5.88e-07!37;UBERON:0000923!6.31e-07!604;UBERON:0005291!6.31e-07!604;UBERON:0006598!6.31e-07!604;UBERON:0002532!6.31e-07!604;UBERON:0001557!7.74e-07!19
|ontology_enrichment_uberon=UBERON:0004119!9.02e-29!169;UBERON:0000925!9.02e-29!169;UBERON:0006595!9.02e-29!169;UBERON:0001007!1.52e-23!155;UBERON:0001555!1.52e-23!155;UBERON:0007026!1.52e-23!155;UBERON:0004921!2.44e-20!129;UBERON:0004185!2.44e-20!129;UBERON:0000077!3.15e-17!130;UBERON:0001004!1.56e-16!72;UBERON:0001041!2.46e-13!98;UBERON:0000065!2.46e-13!53;UBERON:0000062!2.20e-11!511;UBERON:0005911!1.76e-10!82;UBERON:0000464!2.13e-10!104;UBERON:0000072!4.50e-10!46;UBERON:0008947!1.16e-09!38;UBERON:0003258!1.16e-09!38;UBERON:0001048!2.03e-09!168;UBERON:0000466!3.30e-09!126;UBERON:0000161!5.25e-09!35;UBERON:0000922!8.15e-09!612;UBERON:0000481!1.27e-08!347;UBERON:0000468!1.62e-08!659;UBERON:0003104!2.44e-08!238;UBERON:0009142!2.44e-08!238;UBERON:0000344!3.70e-08!12;UBERON:0000160!3.89e-08!27;UBERON:0000064!4.10e-08!219;UBERON:0005409!7.18e-08!35;UBERON:0000166!9.76e-08!21;UBERON:0005177!2.87e-07!107;UBERON:0002050!3.65e-07!605;UBERON:0005423!3.65e-07!605;UBERON:0005153!5.88e-07!37;UBERON:0000923!6.31e-07!604;UBERON:0005291!6.31e-07!604;UBERON:0006598!6.31e-07!604;UBERON:0002532!6.31e-07!604;UBERON:0001557!7.74e-07!19
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327486509535758!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295891974095374!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645356721706507!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00618643543303465!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110064055147428
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}}
}}

Revision as of 14:19, 5 September 2012


Full id: C4617_immature_malignant_squamous_oral_amniotic_Keratinocyte_epidermoid



Phase1 CAGE Peaks

Hg19::chr6:54711471..54711486,+p3@FAM83B
Hg19::chr6:54711509..54711522,+p2@FAM83B
Hg19::chr6:54711533..54711580,+p1@FAM83B


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 cell7.13e-35254
endo-epithelial cell1.34e-2143
endodermal cell6.83e-1759
epithelial cell of alimentary canal7.29e-1321
respiratory epithelial cell8.27e-0813
general ecto-epithelial cell6.22e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.02e-29169
endoderm9.02e-29169
presumptive endoderm9.02e-29169
digestive system1.52e-23155
digestive tract1.52e-23155
primitive gut1.52e-23155
subdivision of digestive tract2.44e-20129
endodermal part of digestive tract2.44e-20129
mixed endoderm/mesoderm-derived structure3.15e-17130
respiratory system1.56e-1672
foregut2.46e-1398
respiratory tract2.46e-1353
organ2.20e-11511
endo-epithelium1.76e-1082
anatomical space2.13e-10104
segment of respiratory tract4.50e-1046
respiratory primordium1.16e-0938
endoderm of foregut1.16e-0938
primordium2.03e-09168
immaterial anatomical entity3.30e-09126
orifice5.25e-0935
embryo8.15e-09612
multi-tissue structure1.27e-08347
multi-cellular organism1.62e-08659
mesenchyme2.44e-08238
entire embryonic mesenchyme2.44e-08238
mucosa3.70e-0812
intestine3.89e-0827
organ part4.10e-08219
gastrointestinal system7.18e-0835
oral opening9.76e-0821
trunk region element2.87e-07107
embryonic structure3.65e-07605
developing anatomical structure3.65e-07605
epithelial bud5.88e-0737
germ layer6.31e-07604
embryonic tissue6.31e-07604
presumptive structure6.31e-07604
epiblast (generic)6.31e-07604
upper respiratory tract7.74e-0719
Disease
Ontology termp-valuen
carcinoma3.04e-24106
cell type cancer1.26e-17143
adenocarcinoma2.93e-1025
squamous cell carcinoma3.69e-1014
cancer7.87e-07235
disease of cellular proliferation8.60e-07239


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#186934.907389214879320.008460985347239390.0327486509535758
MYC#460935.22228187160940.007020843755740150.0295891974095374
STAT3#6774310.51946499715420.0008589184530415310.00645356721706507
TFAP2C#7022310.80922860986020.0007916746575753130.00618643543303465
ZNF263#1012738.221841637010680.001799043925565870.0110064055147428



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.