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Coexpression cluster:C1451: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001004!5.30e-18!74;UBERON:0004119!1.56e-15!160;UBERON:0000925!1.56e-15!160;UBERON:0006595!1.56e-15!160;UBERON:0000166!6.05e-14!22;UBERON:0000161!6.01e-13!36;UBERON:0003102!6.86e-13!99;UBERON:0000065!4.96e-12!54;UBERON:0000165!1.54e-11!29;UBERON:0000930!1.54e-11!29;UBERON:0000365!2.40e-11!5;UBERON:0000153!4.87e-11!62;UBERON:0007811!4.87e-11!62;UBERON:0000344!7.32e-11!20;UBERON:0007196!1.34e-10!15;UBERON:0001558!1.34e-10!15;UBERON:0003729!9.22e-10!13;UBERON:0005910!2.28e-09!6;UBERON:0000033!2.48e-09!56;UBERON:0001007!4.51e-09!145;UBERON:0001555!4.51e-09!145;UBERON:0007026!4.51e-09!145;UBERON:0000974!7.07e-09!10;UBERON:0000072!8.27e-09!47;UBERON:0003343!1.51e-08!4;UBERON:0004785!1.51e-08!4;UBERON:0006562!2.54e-08!11;UBERON:0001949!4.18e-08!3;UBERON:0004815!5.13e-08!3;UBERON:0002031!5.13e-08!3;UBERON:0005178!5.27e-08!34;UBERON:0002224!5.27e-08!34;UBERON:0003126!7.80e-08!7;UBERON:0001005!7.80e-08!7;UBERON:0005181!1.09e-07!35;UBERON:0001444!1.23e-07!49;UBERON:0001723!3.32e-07!3;UBERON:0001033!3.32e-07!3;UBERON:0010056!3.32e-07!3;UBERON:0004807!5.26e-07!28;UBERON:0000475!7.16e-07!264;UBERON:0001042!7.17e-07!10;UBERON:0009145!7.17e-07!10
|ontology_enrichment_uberon=UBERON:0001004!5.30e-18!74;UBERON:0004119!1.56e-15!160;UBERON:0000925!1.56e-15!160;UBERON:0006595!1.56e-15!160;UBERON:0000166!6.05e-14!22;UBERON:0000161!6.01e-13!36;UBERON:0003102!6.86e-13!99;UBERON:0000065!4.96e-12!54;UBERON:0000165!1.54e-11!29;UBERON:0000930!1.54e-11!29;UBERON:0000365!2.40e-11!5;UBERON:0000153!4.87e-11!62;UBERON:0007811!4.87e-11!62;UBERON:0000344!7.32e-11!20;UBERON:0007196!1.34e-10!15;UBERON:0001558!1.34e-10!15;UBERON:0003729!9.22e-10!13;UBERON:0005910!2.28e-09!6;UBERON:0000033!2.48e-09!56;UBERON:0001007!4.51e-09!145;UBERON:0001555!4.51e-09!145;UBERON:0007026!4.51e-09!145;UBERON:0000974!7.07e-09!10;UBERON:0000072!8.27e-09!47;UBERON:0003343!1.51e-08!4;UBERON:0004785!1.51e-08!4;UBERON:0006562!2.54e-08!11;UBERON:0001949!4.18e-08!3;UBERON:0004815!5.13e-08!3;UBERON:0002031!5.13e-08!3;UBERON:0005178!5.27e-08!34;UBERON:0002224!5.27e-08!34;UBERON:0003126!7.80e-08!7;UBERON:0001005!7.80e-08!7;UBERON:0005181!1.09e-07!35;UBERON:0001444!1.23e-07!49;UBERON:0001723!3.32e-07!3;UBERON:0001033!3.32e-07!3;UBERON:0010056!3.32e-07!3;UBERON:0004807!5.26e-07!28;UBERON:0000475!7.16e-07!264;UBERON:0001042!7.17e-07!10;UBERON:0009145!7.17e-07!10
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}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1451_immature_Sebocyte_squamous_Keratinocyte_Corneal_Small_Urothelial



Phase1 CAGE Peaks

Hg19::chr19:3136918..3136931,-p@chr19:3136918..3136931
-
Hg19::chr1:153321301..153321325,-p1@PGLYRP4
Hg19::chr1:24646263..24646277,+p4@GRHL3
Hg19::chr1:27188807..27188826,+p@chr1:27188807..27188826
+
Hg19::chr1:6550625..6550646,-p3@PLEKHG5
Hg19::chr20:33880219..33880234,-p1@FAM83C


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:0008745N-acetylmuramoyl-L-alanine amidase activity0.00976204444926934
GO:0016019peptidoglycan receptor activity0.00976204444926934
GO:0009253peptidoglycan catabolic process0.00976204444926934
GO:0000270peptidoglycan metabolic process0.00976204444926934
GO:0050830defense response to Gram-positive bacterium0.00976204444926934
GO:0016045detection of bacterium0.00976204444926934
GO:0042834peptidoglycan binding0.00976204444926934
GO:0008329pattern recognition receptor activity0.0113880460240682
GO:0009595detection of biotic stimulus0.0118091301495636
GO:0009581detection of external stimulus0.0379177019804636



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>

Uber Anatomy
Ontology termp-valuen
respiratory system5.30e-1874
endoderm-derived structure1.56e-15160
endoderm1.56e-15160
presumptive endoderm1.56e-15160
oral opening6.05e-1422
orifice6.01e-1336
surface structure6.86e-1399
respiratory tract4.96e-1254
mouth1.54e-1129
stomodeum1.54e-1129
urothelium2.40e-115
anterior region of body4.87e-1162
craniocervical region4.87e-1162
mucosa7.32e-1120
tracheobronchial tree1.34e-1015
lower respiratory tract1.34e-1015
mouth mucosa9.22e-1013
transitional epithelium2.28e-096
head2.48e-0956
digestive system4.51e-09145
digestive tract4.51e-09145
primitive gut4.51e-09145
neck7.07e-0910
segment of respiratory tract8.27e-0947
mucosa of oral region1.51e-084
respiratory system mucosa1.51e-084
pharynx2.54e-0811
gingival epithelium4.18e-083
lower respiratory tract epithelium5.13e-083
epithelium of bronchus5.13e-083
thoracic cavity element5.27e-0834
thoracic cavity5.27e-0834
trachea7.80e-087
respiratory airway7.80e-087
thoracic segment organ1.09e-0735
subdivision of head1.23e-0749
tongue3.32e-073
gustatory system3.32e-073
future tongue3.32e-073
respiratory system epithelium5.26e-0728
organism subdivision7.16e-07264
chordate pharynx7.17e-0710
pharyngeal region of foregut7.17e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma6.55e-1914


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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