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Coexpression cluster:C3242: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004815!4.25e-27!3;UBERON:0002031!4.25e-27!3;UBERON:0002185!1.62e-16!5;UBERON:0007196!1.19e-14!15;UBERON:0001558!1.19e-14!15;UBERON:0001949!1.41e-12!3;UBERON:0001004!1.76e-12!74;UBERON:0003729!6.39e-11!13;UBERON:0003102!1.20e-10!99;UBERON:0001708!8.26e-10!4;UBERON:0008895!8.26e-10!4;UBERON:0000964!1.52e-09!4;UBERON:0010409!1.52e-09!4;UBERON:0004348!1.52e-09!4;UBERON:0005427!1.52e-09!4;UBERON:0004119!1.52e-09!160;UBERON:0000925!1.52e-09!160;UBERON:0006595!1.52e-09!160;UBERON:0000485!2.04e-09!9;UBERON:0000065!2.33e-09!54;UBERON:0000033!6.50e-09!56;UBERON:0011159!5.12e-08!5;UBERON:0000153!5.95e-08!62;UBERON:0007811!5.95e-08!62;UBERON:0000365!8.04e-08!5;UBERON:0004807!1.04e-07!28;UBERON:0000344!3.77e-07!20;UBERON:0010188!8.15e-07!6;UBERON:0002539!8.15e-07!6;UBERON:0008816!8.15e-07!6
|ontology_enrichment_uberon=UBERON:0004815!4.25e-27!3;UBERON:0002031!4.25e-27!3;UBERON:0002185!1.62e-16!5;UBERON:0007196!1.19e-14!15;UBERON:0001558!1.19e-14!15;UBERON:0001949!1.41e-12!3;UBERON:0001004!1.76e-12!74;UBERON:0003729!6.39e-11!13;UBERON:0003102!1.20e-10!99;UBERON:0001708!8.26e-10!4;UBERON:0008895!8.26e-10!4;UBERON:0000964!1.52e-09!4;UBERON:0010409!1.52e-09!4;UBERON:0004348!1.52e-09!4;UBERON:0005427!1.52e-09!4;UBERON:0004119!1.52e-09!160;UBERON:0000925!1.52e-09!160;UBERON:0006595!1.52e-09!160;UBERON:0000485!2.04e-09!9;UBERON:0000065!2.33e-09!54;UBERON:0000033!6.50e-09!56;UBERON:0011159!5.12e-08!5;UBERON:0000153!5.95e-08!62;UBERON:0007811!5.95e-08!62;UBERON:0000365!8.04e-08!5;UBERON:0004807!1.04e-07!28;UBERON:0000344!3.77e-07!20;UBERON:0010188!8.15e-07!6;UBERON:0002539!8.15e-07!6;UBERON:0008816!8.15e-07!6
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}}
}}

Revision as of 16:00, 26 November 2012


Full id: C3242_Small_Tracheal_Bronchial_Mallassezderived_Keratinocyte_Gingival_Mammary



Phase1 CAGE Peaks

Hg19::chr12:116955659..116955671,+p1@ENST00000552992
Hg19::chr12:28187330..28187352,-p@chr12:28187330..28187352
-
Hg19::chr14:85799279..85799283,+p@chr14:85799279..85799283
+


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
respiratory epithelial cell5.63e-4213
endo-epithelial cell1.08e-3242
general ecto-epithelial cell6.01e-3014
bronchial epithelial cell4.25e-273
epithelial cell of tracheobronchial tree1.81e-249
epithelial cell of lower respiratory tract1.81e-249
endodermal cell4.34e-2358
corneal epithelial cell3.77e-182
epithelial cell6.89e-15253
stratified squamous epithelial cell7.00e-146
keratin accumulating cell7.00e-146
stratified epithelial cell7.00e-146
keratinizing barrier epithelial cell7.00e-146
epithelial fate stem cell7.00e-146
stratified epithelial stem cell7.00e-146
surface ectodermal cell7.00e-146
duct epithelial cell7.86e-133
branched duct epithelial cell7.86e-133
tracheal epithelial cell7.86e-133
tracheoblast7.86e-133
epithelial cell of Malassez8.84e-133
gingival epithelial cell1.41e-123
ecto-epithelial cell6.40e-1234
embryonic cell1.25e-10250
buccal mucosa cell3.71e-101
endothelial cell of viscerocranial mucosa3.71e-101
keratinized cell of the oral mucosa3.71e-101
transitional epithelial cell1.46e-094
urothelial cell1.46e-094
epidermal cell1.82e-099
keratinocyte4.78e-085
squamous epithelial cell8.10e-0863
epithelial cell of alimentary canal3.77e-0720
Uber Anatomy
Ontology termp-valuen
lower respiratory tract epithelium4.25e-273
epithelium of bronchus4.25e-273
bronchus1.62e-165
tracheobronchial tree1.19e-1415
lower respiratory tract1.19e-1415
gingival epithelium1.41e-123
respiratory system1.76e-1274
mouth mucosa6.39e-1113
surface structure1.20e-1099
jaw skeleton8.26e-104
splanchnocranium8.26e-104
cornea1.52e-094
eye surface1.52e-094
optic eminence1.52e-094
corneal primordium1.52e-094
endoderm-derived structure1.52e-09160
endoderm1.52e-09160
presumptive endoderm1.52e-09160
simple columnar epithelium2.04e-099
respiratory tract2.33e-0954
head6.50e-0956
primary subdivision of cranial skeletal system5.12e-085
anterior region of body5.95e-0862
craniocervical region5.95e-0862
urothelium8.04e-085
respiratory system epithelium1.04e-0728
mucosa3.77e-0720
protuberance8.15e-076
pharyngeal arch8.15e-076
embryonic head8.15e-076


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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