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Coexpression cluster:C3417: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001004!2.56e-23!74;UBERON:0000065!1.48e-16!54;UBERON:0000153!6.12e-16!62;UBERON:0007811!6.12e-16!62;UBERON:0000166!7.60e-16!22;UBERON:0004119!1.57e-15!160;UBERON:0000925!1.57e-15!160;UBERON:0006595!1.57e-15!160;UBERON:0003102!2.43e-14!99;UBERON:0000161!1.55e-13!36;UBERON:0000165!1.88e-13!29;UBERON:0000930!1.88e-13!29;UBERON:0000974!8.03e-12!10;UBERON:0000033!9.24e-12!56;UBERON:0007196!6.05e-11!15;UBERON:0001558!6.05e-11!15;UBERON:0005178!8.70e-11!34;UBERON:0002224!8.70e-11!34;UBERON:0005181!2.17e-10!35;UBERON:0003126!4.66e-10!7;UBERON:0001005!4.66e-10!7;UBERON:0001007!8.27e-10!145;UBERON:0001555!8.27e-10!145;UBERON:0007026!8.27e-10!145;UBERON:0001041!1.15e-09!87;UBERON:0001444!2.12e-09!49;UBERON:0004815!2.36e-09!3;UBERON:0002031!2.36e-09!3;UBERON:0003729!2.43e-09!13;UBERON:0001042!3.22e-09!10;UBERON:0009145!3.22e-09!10;UBERON:0001949!3.39e-09!3;UBERON:0000365!3.85e-09!5;UBERON:0001723!9.49e-09!3;UBERON:0001033!9.49e-09!3;UBERON:0010056!9.49e-09!3;UBERON:0008814!2.59e-08!18;UBERON:0006562!2.59e-08!11;UBERON:0000072!2.84e-08!47;UBERON:0000475!4.19e-08!264;UBERON:0005157!6.45e-08!47;UBERON:0004921!7.58e-08!118;UBERON:0005910!1.31e-07!6;UBERON:0005153!1.32e-07!37;UBERON:0000344!1.69e-07!20;UBERON:0003408!6.28e-07!10;UBERON:0001708!7.45e-07!4;UBERON:0008895!7.45e-07!4;UBERON:0001911!9.09e-07!4;UBERON:0005333!9.09e-07!4;UBERON:0008425!9.09e-07!4;UBERON:0005311!9.09e-07!4
|ontology_enrichment_uberon=UBERON:0001004!2.56e-23!74;UBERON:0000065!1.48e-16!54;UBERON:0000153!6.12e-16!62;UBERON:0007811!6.12e-16!62;UBERON:0000166!7.60e-16!22;UBERON:0004119!1.57e-15!160;UBERON:0000925!1.57e-15!160;UBERON:0006595!1.57e-15!160;UBERON:0003102!2.43e-14!99;UBERON:0000161!1.55e-13!36;UBERON:0000165!1.88e-13!29;UBERON:0000930!1.88e-13!29;UBERON:0000974!8.03e-12!10;UBERON:0000033!9.24e-12!56;UBERON:0007196!6.05e-11!15;UBERON:0001558!6.05e-11!15;UBERON:0005178!8.70e-11!34;UBERON:0002224!8.70e-11!34;UBERON:0005181!2.17e-10!35;UBERON:0003126!4.66e-10!7;UBERON:0001005!4.66e-10!7;UBERON:0001007!8.27e-10!145;UBERON:0001555!8.27e-10!145;UBERON:0007026!8.27e-10!145;UBERON:0001041!1.15e-09!87;UBERON:0001444!2.12e-09!49;UBERON:0004815!2.36e-09!3;UBERON:0002031!2.36e-09!3;UBERON:0003729!2.43e-09!13;UBERON:0001042!3.22e-09!10;UBERON:0009145!3.22e-09!10;UBERON:0001949!3.39e-09!3;UBERON:0000365!3.85e-09!5;UBERON:0001723!9.49e-09!3;UBERON:0001033!9.49e-09!3;UBERON:0010056!9.49e-09!3;UBERON:0008814!2.59e-08!18;UBERON:0006562!2.59e-08!11;UBERON:0000072!2.84e-08!47;UBERON:0000475!4.19e-08!264;UBERON:0005157!6.45e-08!47;UBERON:0004921!7.58e-08!118;UBERON:0005910!1.31e-07!6;UBERON:0005153!1.32e-07!37;UBERON:0000344!1.69e-07!20;UBERON:0003408!6.28e-07!10;UBERON:0001708!7.45e-07!4;UBERON:0008895!7.45e-07!4;UBERON:0001911!9.09e-07!4;UBERON:0005333!9.09e-07!4;UBERON:0008425!9.09e-07!4;UBERON:0005311!9.09e-07!4
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}}
}}

Revision as of 16:07, 26 November 2012


Full id: C3417_salivary_Corneal_tongue_Bronchial_esophagus_Esophageal_immature



Phase1 CAGE Peaks

Hg19::chr14:24779340..24779371,+p1@LTB4R2
Hg19::chr14:24779376..24779394,+p2@LTB4R2
Hg19::chr17:39738633..39738657,-p@chr17:39738633..39738657
-


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><br>

Cell Type
Ontology termp-valuen
endo-epithelial cell4.32e-2942
respiratory epithelial cell1.04e-1913
endodermal cell2.87e-1958
general ecto-epithelial cell1.60e-1814
epithelial cell of alimentary canal7.38e-1520
acinar cell1.91e-145
protein secreting cell5.78e-126
transitional epithelial cell1.96e-114
urothelial cell1.96e-114
epithelial cell of tracheobronchial tree4.65e-119
epithelial cell of lower respiratory tract4.65e-119
epithelial cell1.39e-10253
acinar cell of salivary gland7.02e-103
duct epithelial cell2.36e-093
branched duct epithelial cell2.36e-093
bronchial epithelial cell2.36e-093
tracheal epithelial cell2.36e-093
tracheoblast2.36e-093
gingival epithelial cell3.39e-093
ecto-epithelial cell3.40e-0934
epithelial cell of Malassez4.97e-093
stratified squamous epithelial cell5.61e-086
keratin accumulating cell5.61e-086
stratified epithelial cell5.61e-086
keratinizing barrier epithelial cell5.61e-086
epithelial fate stem cell5.61e-086
stratified epithelial stem cell5.61e-086
surface ectodermal cell5.61e-086
glandular epithelial cell7.99e-089
epidermal cell1.32e-079
corneal epithelial cell3.25e-072
mammary gland epithelial cell9.09e-074
Uber Anatomy
Ontology termp-valuen
respiratory system2.56e-2374
respiratory tract1.48e-1654
anterior region of body6.12e-1662
craniocervical region6.12e-1662
oral opening7.60e-1622
endoderm-derived structure1.57e-15160
endoderm1.57e-15160
presumptive endoderm1.57e-15160
surface structure2.43e-1499
orifice1.55e-1336
mouth1.88e-1329
stomodeum1.88e-1329
neck8.03e-1210
head9.24e-1256
tracheobronchial tree6.05e-1115
lower respiratory tract6.05e-1115
thoracic cavity element8.70e-1134
thoracic cavity8.70e-1134
thoracic segment organ2.17e-1035
trachea4.66e-107
respiratory airway4.66e-107
digestive system8.27e-10145
digestive tract8.27e-10145
primitive gut8.27e-10145
foregut1.15e-0987
subdivision of head2.12e-0949
lower respiratory tract epithelium2.36e-093
epithelium of bronchus2.36e-093
mouth mucosa2.43e-0913
chordate pharynx3.22e-0910
pharyngeal region of foregut3.22e-0910
gingival epithelium3.39e-093
urothelium3.85e-095
tongue9.49e-093
gustatory system9.49e-093
future tongue9.49e-093
pharyngeal arch system2.59e-0818
pharynx2.59e-0811
segment of respiratory tract2.84e-0847
organism subdivision4.19e-08264
epithelial fold6.45e-0847
subdivision of digestive tract7.58e-08118
transitional epithelium1.31e-076
epithelial bud1.32e-0737
mucosa1.69e-0720
gland of gut6.28e-0710
jaw skeleton7.45e-074
splanchnocranium7.45e-074
mammary gland9.09e-074
mammary bud9.09e-074
mammary ridge9.09e-074
mammary placode9.09e-074


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

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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