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Coexpression cluster:C2561: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001004!9.08e-15!74;UBERON:0003135!2.51e-14!11;UBERON:0000166!4.29e-13!22;UBERON:0000161!5.40e-13!36;UBERON:0004119!8.15e-13!160;UBERON:0000925!8.15e-13!160;UBERON:0006595!8.15e-13!160;UBERON:0000365!5.05e-12!5;UBERON:0003101!5.18e-12!22;UBERON:0000079!5.18e-12!22;UBERON:0000165!4.62e-11!29;UBERON:0000930!4.62e-11!29;UBERON:0003729!1.01e-10!13;UBERON:0003102!1.66e-10!99;UBERON:0000153!4.08e-10!62;UBERON:0007811!4.08e-10!62;UBERON:0005910!6.07e-10!6;UBERON:0000344!1.01e-09!20;UBERON:0003343!1.15e-09!4;UBERON:0004785!1.15e-09!4;UBERON:0000033!2.15e-09!56;UBERON:0000473!4.30e-09!8;UBERON:0000065!2.50e-08!54;UBERON:0004815!2.92e-08!3;UBERON:0002031!2.92e-08!3;UBERON:0001949!3.63e-08!3;UBERON:0001007!7.93e-08!145;UBERON:0001555!7.93e-08!145;UBERON:0007026!7.93e-08!145;UBERON:0000974!1.72e-07!10;UBERON:0001444!1.90e-07!49;UBERON:0006947!2.17e-07!3;UBERON:0004054!2.17e-07!3;UBERON:0007196!7.14e-07!15;UBERON:0001558!7.14e-07!15;UBERON:0000464!9.71e-07!95
|ontology_enrichment_uberon=UBERON:0001004!9.08e-15!74;UBERON:0003135!2.51e-14!11;UBERON:0000166!4.29e-13!22;UBERON:0000161!5.40e-13!36;UBERON:0004119!8.15e-13!160;UBERON:0000925!8.15e-13!160;UBERON:0006595!8.15e-13!160;UBERON:0000365!5.05e-12!5;UBERON:0003101!5.18e-12!22;UBERON:0000079!5.18e-12!22;UBERON:0000165!4.62e-11!29;UBERON:0000930!4.62e-11!29;UBERON:0003729!1.01e-10!13;UBERON:0003102!1.66e-10!99;UBERON:0000153!4.08e-10!62;UBERON:0007811!4.08e-10!62;UBERON:0005910!6.07e-10!6;UBERON:0000344!1.01e-09!20;UBERON:0003343!1.15e-09!4;UBERON:0004785!1.15e-09!4;UBERON:0000033!2.15e-09!56;UBERON:0000473!4.30e-09!8;UBERON:0000065!2.50e-08!54;UBERON:0004815!2.92e-08!3;UBERON:0002031!2.92e-08!3;UBERON:0001949!3.63e-08!3;UBERON:0001007!7.93e-08!145;UBERON:0001555!7.93e-08!145;UBERON:0007026!7.93e-08!145;UBERON:0000974!1.72e-07!10;UBERON:0001444!1.90e-07!49;UBERON:0006947!2.17e-07!3;UBERON:0004054!2.17e-07!3;UBERON:0007196!7.14e-07!15;UBERON:0001558!7.14e-07!15;UBERON:0000464!9.71e-07!95
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2561_Prostate_Small_salivary_oral_Bronchial_nasal_squamous



Phase1 CAGE Peaks

Hg19::chr1:209602609..209602628,+p3@ENST00000458250
Hg19::chr1:209602671..209602695,+p1@ENST00000458250
Hg19::chr1:209603797..209603808,+p1@AK002208
Hg19::chr6:56505212..56505242,-p@chr6:56505212..56505242
-


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 cell7.32e-3642
endodermal cell1.27e-2558
epithelial cell1.22e-22253
epithelial cell of alimentary canal1.14e-2020
respiratory epithelial cell6.69e-1813
general ecto-epithelial cell5.89e-1314
acinar cell8.41e-135
protein secreting cell1.39e-106
transitional epithelial cell2.09e-104
urothelial cell2.09e-104
epithelial cell of tracheobronchial tree2.26e-099
epithelial cell of lower respiratory tract2.26e-099
ecto-epithelial cell4.23e-0934
squamous epithelial cell1.32e-0863
acinar cell of salivary gland1.67e-083
bronchial epithelial cell2.92e-083
epithelial cell of Malassez3.54e-083
gingival epithelial cell3.63e-083
duct epithelial cell6.56e-083
branched duct epithelial cell6.56e-083
tracheal epithelial cell6.56e-083
tracheoblast6.56e-083
embryonic cell1.71e-07250
germ line cell2.28e-077
germ cell2.28e-077
glandular epithelial cell7.02e-079
Uber Anatomy
Ontology termp-valuen
respiratory system9.08e-1574
male reproductive organ2.51e-1411
oral opening4.29e-1322
orifice5.40e-1336
endoderm-derived structure8.15e-13160
endoderm8.15e-13160
presumptive endoderm8.15e-13160
urothelium5.05e-125
male organism5.18e-1222
male reproductive system5.18e-1222
mouth4.62e-1129
stomodeum4.62e-1129
mouth mucosa1.01e-1013
surface structure1.66e-1099
anterior region of body4.08e-1062
craniocervical region4.08e-1062
transitional epithelium6.07e-106
mucosa1.01e-0920
mucosa of oral region1.15e-094
respiratory system mucosa1.15e-094
head2.15e-0956
testis4.30e-098
respiratory tract2.50e-0854
lower respiratory tract epithelium2.92e-083
epithelium of bronchus2.92e-083
gingival epithelium3.63e-083
digestive system7.93e-08145
digestive tract7.93e-08145
primitive gut7.93e-08145
neck1.72e-0710
subdivision of head1.90e-0749
male genital duct2.17e-073
internal male genitalia2.17e-073
tracheobronchial tree7.14e-0715
lower respiratory tract7.14e-0715
anatomical space9.71e-0795
Disease
Ontology termp-valuen
squamous cell carcinoma4.60e-2114


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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