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Coexpression cluster:C4386: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004815!4.11e-18!3;UBERON:0002031!4.11e-18!3;UBERON:0007196!5.38e-18!15;UBERON:0001558!5.38e-18!15;UBERON:0001949!1.52e-17!3;UBERON:0001004!4.84e-16!74;UBERON:0003729!3.31e-15!13;UBERON:0000344!7.03e-13!20;UBERON:0000072!2.03e-12!47;UBERON:0000166!1.13e-11!22;UBERON:0000165!2.91e-11!29;UBERON:0000930!2.91e-11!29;UBERON:0003102!3.17e-11!99;UBERON:0000161!3.99e-11!36;UBERON:0002185!4.52e-11!5;UBERON:0001007!4.70e-11!145;UBERON:0001555!4.70e-11!145;UBERON:0007026!4.70e-11!145;UBERON:0004119!7.36e-11!160;UBERON:0000925!7.36e-11!160;UBERON:0006595!7.36e-11!160;UBERON:0000153!1.18e-10!62;UBERON:0007811!1.18e-10!62;UBERON:0008947!1.43e-10!38;UBERON:0003258!1.43e-10!38;UBERON:0000065!1.54e-10!54;UBERON:0000033!4.37e-10!56;UBERON:0005178!1.50e-09!34;UBERON:0002224!1.50e-09!34;UBERON:0005181!3.04e-09!35;UBERON:0004807!4.48e-09!28;UBERON:0003126!4.71e-08!7;UBERON:0001005!4.71e-08!7;UBERON:0001444!8.04e-08!49;UBERON:0001041!6.11e-07!87;UBERON:0003350!7.12e-07!8;UBERON:0001828!7.12e-07!8
|ontology_enrichment_uberon=UBERON:0004815!4.11e-18!3;UBERON:0002031!4.11e-18!3;UBERON:0007196!5.38e-18!15;UBERON:0001558!5.38e-18!15;UBERON:0001949!1.52e-17!3;UBERON:0001004!4.84e-16!74;UBERON:0003729!3.31e-15!13;UBERON:0000344!7.03e-13!20;UBERON:0000072!2.03e-12!47;UBERON:0000166!1.13e-11!22;UBERON:0000165!2.91e-11!29;UBERON:0000930!2.91e-11!29;UBERON:0003102!3.17e-11!99;UBERON:0000161!3.99e-11!36;UBERON:0002185!4.52e-11!5;UBERON:0001007!4.70e-11!145;UBERON:0001555!4.70e-11!145;UBERON:0007026!4.70e-11!145;UBERON:0004119!7.36e-11!160;UBERON:0000925!7.36e-11!160;UBERON:0006595!7.36e-11!160;UBERON:0000153!1.18e-10!62;UBERON:0007811!1.18e-10!62;UBERON:0008947!1.43e-10!38;UBERON:0003258!1.43e-10!38;UBERON:0000065!1.54e-10!54;UBERON:0000033!4.37e-10!56;UBERON:0005178!1.50e-09!34;UBERON:0002224!1.50e-09!34;UBERON:0005181!3.04e-09!35;UBERON:0004807!4.48e-09!28;UBERON:0003126!4.71e-08!7;UBERON:0001005!4.71e-08!7;UBERON:0001444!8.04e-08!49;UBERON:0001041!6.11e-07!87;UBERON:0003350!7.12e-07!8;UBERON:0001828!7.12e-07!8
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}}
}}

Revision as of 16:42, 26 November 2012


Full id: C4386_Bronchial_Keratinocyte_Sebocyte_oral_tongue_Tracheal_Prostate



Phase1 CAGE Peaks

Hg19::chr4:15938017..15938029,-p1@AB464521
Hg19::chr4:15938074..15938085,-p3@AB464521
Hg19::chr4:15938120..15938127,-p5@AB464521


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
endo-epithelial cell3.03e-3142
epithelial cell of tracheobronchial tree1.43e-309
epithelial cell of lower respiratory tract1.43e-309
endodermal cell1.14e-2158
respiratory epithelial cell6.69e-2113
duct epithelial cell3.66e-183
branched duct epithelial cell3.66e-183
tracheal epithelial cell3.66e-183
tracheoblast3.66e-183
bronchial epithelial cell4.11e-183
gingival epithelial cell1.52e-173
epithelial cell2.11e-15253
general ecto-epithelial cell2.29e-1414
epithelial cell of alimentary canal1.10e-0920
stratified squamous epithelial cell2.45e-096
keratin accumulating cell2.45e-096
stratified epithelial cell2.45e-096
keratinizing barrier epithelial cell2.45e-096
epithelial fate stem cell2.45e-096
stratified epithelial stem cell2.45e-096
surface ectodermal cell2.45e-096
squamous epithelial cell1.04e-0863
epithelial cell of Malassez1.54e-083
epithelial cell of prostate2.08e-083
buccal mucosa cell4.01e-071
endothelial cell of viscerocranial mucosa4.01e-071
keratinized cell of the oral mucosa4.01e-071
Uber Anatomy
Ontology termp-valuen
lower respiratory tract epithelium4.11e-183
epithelium of bronchus4.11e-183
tracheobronchial tree5.38e-1815
lower respiratory tract5.38e-1815
gingival epithelium1.52e-173
respiratory system4.84e-1674
mouth mucosa3.31e-1513
mucosa7.03e-1320
segment of respiratory tract2.03e-1247
oral opening1.13e-1122
mouth2.91e-1129
stomodeum2.91e-1129
surface structure3.17e-1199
orifice3.99e-1136
bronchus4.52e-115
digestive system4.70e-11145
digestive tract4.70e-11145
primitive gut4.70e-11145
endoderm-derived structure7.36e-11160
endoderm7.36e-11160
presumptive endoderm7.36e-11160
anterior region of body1.18e-1062
craniocervical region1.18e-1062
respiratory primordium1.43e-1038
endoderm of foregut1.43e-1038
respiratory tract1.54e-1054
head4.37e-1056
thoracic cavity element1.50e-0934
thoracic cavity1.50e-0934
thoracic segment organ3.04e-0935
respiratory system epithelium4.48e-0928
trachea4.71e-087
respiratory airway4.71e-087
subdivision of head8.04e-0849
foregut6.11e-0787
epithelium of mucosa7.12e-078
gingiva7.12e-078
Disease
Ontology termp-valuen
squamous cell carcinoma1.40e-1314


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

No analysis results for this cluster

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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