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Coexpression cluster:C683: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.17e-08!106;DOID:1749!1.47e-07!14
|ontology_enrichment_disease=DOID:305!4.17e-08!106;DOID:1749!1.47e-07!14
|ontology_enrichment_uberon=UBERON:0004119!4.18e-12!169;UBERON:0000925!4.18e-12!169;UBERON:0006595!4.18e-12!169;UBERON:0000064!1.55e-10!219;UBERON:0000062!6.88e-10!511;UBERON:0000464!1.29e-09!104;UBERON:0001004!1.51e-09!72;UBERON:0001007!3.41e-08!155;UBERON:0001555!3.41e-08!155;UBERON:0007026!3.41e-08!155;UBERON:0000077!8.03e-08!130;UBERON:0000466!8.29e-08!126;UBERON:0000161!9.65e-08!35;UBERON:0004921!1.15e-07!129;UBERON:0004185!1.15e-07!129;UBERON:0007023!1.16e-07!115;UBERON:0000468!1.83e-07!659;UBERON:0000922!3.29e-07!612;UBERON:0005177!4.33e-07!107;UBERON:0000475!4.64e-07!365;UBERON:0001008!5.25e-07!45;UBERON:0000166!6.18e-07!21
|ontology_enrichment_uberon=UBERON:0004119!4.18e-12!169;UBERON:0000925!4.18e-12!169;UBERON:0006595!4.18e-12!169;UBERON:0000064!1.55e-10!219;UBERON:0000062!6.88e-10!511;UBERON:0000464!1.29e-09!104;UBERON:0001004!1.51e-09!72;UBERON:0001007!3.41e-08!155;UBERON:0001555!3.41e-08!155;UBERON:0007026!3.41e-08!155;UBERON:0000077!8.03e-08!130;UBERON:0000466!8.29e-08!126;UBERON:0000161!9.65e-08!35;UBERON:0004921!1.15e-07!129;UBERON:0004185!1.15e-07!129;UBERON:0007023!1.16e-07!115;UBERON:0000468!1.83e-07!659;UBERON:0000922!3.29e-07!612;UBERON:0005177!4.33e-07!107;UBERON:0000475!4.64e-07!365;UBERON:0001008!5.25e-07!45;UBERON:0000166!6.18e-07!21
|tf_chipseq_enrich=MAFK#7975;3:6.77518328445748:0.00860006079038526:0.0327624201673188
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}}
}}

Revision as of 12:49, 5 September 2012


Full id: C683_esophagus_tongue_tonsil_Corneal_cervical_Esophageal_throat



Phase1 CAGE Peaks

Hg19::chr11:119039032..119039058,+p5@NLRX1
Hg19::chr11:119039069..119039081,+p9@NLRX1
Hg19::chr14:24732368..24732391,-p1@TGM1
Hg19::chr14:24732403..24732410,-p4@TGM1
Hg19::chr14:24732738..24732753,-p3@TGM1
Hg19::chr1:153285441..153285450,-p@chr1:153285441..153285450
-
Hg19::chr1:24645832..24645853,+p1@GRHL3
Hg19::chr1:24645865..24645871,+p6@GRHL3
Hg19::chr1:24645921..24645973,+p2@GRHL3
Hg19::chr20:33880168..33880183,-p2@FAM83C
Hg19::chr6:53794788..53794806,+p12@MLIP
Hg19::chr7:44029862..44029900,-p1@ENST00000420754


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


GO IDGO nameFDR corrected p-value
GO:0043163cell envelope organization and biogenesis0.0157183645563999
GO:0005913cell-cell adherens junction0.0336544548770559
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.0336544548770559
GO:0001533cornified envelope0.0336544548770559
GO:0045229external encapsulating structure organization and biogenesis0.0336544548770559
GO:0018149peptide cross-linking0.0336544548770559
GO:0030216keratinocyte differentiation0.0336544548770559
GO:0031424keratinization0.0357618532746787
GO:0016755transferase activity, transferring amino-acyl groups0.0357618532746787
GO:0009913epidermal cell differentiation0.0359650815239245
GO:0005912adherens junction0.0359650815239245
GO:0048730epidermis morphogenesis0.0359650815239245
GO:0048729tissue morphogenesis0.0434381461036677



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 cell1.29e-18254
endo-epithelial cell6.23e-1543
endodermal cell2.84e-1159
respiratory epithelial cell2.33e-0813
epithelial cell of alimentary canal1.04e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.18e-12169
endoderm4.18e-12169
presumptive endoderm4.18e-12169
organ part1.55e-10219
organ6.88e-10511
anatomical space1.29e-09104
respiratory system1.51e-0972
digestive system3.41e-08155
digestive tract3.41e-08155
primitive gut3.41e-08155
mixed endoderm/mesoderm-derived structure8.03e-08130
immaterial anatomical entity8.29e-08126
orifice9.65e-0835
subdivision of digestive tract1.15e-07129
endodermal part of digestive tract1.15e-07129
adult organism1.16e-07115
multi-cellular organism1.83e-07659
embryo3.29e-07612
trunk region element4.33e-07107
organism subdivision4.64e-07365
renal system5.25e-0745
oral opening6.18e-0721
Disease
Ontology termp-valuen
carcinoma4.17e-08106
squamous cell carcinoma1.47e-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
MAFK#797536.775183284457480.008600060790385260.0327624201673188



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.