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Coexpression cluster:C1613: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004119!9.24e-25!160;UBERON:0000925!9.24e-25!160;UBERON:0006595!9.24e-25!160;UBERON:0001004!3.81e-23!74;UBERON:0001557!4.86e-20!19;UBERON:0005631!5.40e-18!14;UBERON:0000158!5.40e-18!14;UBERON:0001737!9.49e-18!9;UBERON:0000065!1.13e-16!54;UBERON:0001007!2.90e-16!145;UBERON:0001555!2.90e-16!145;UBERON:0007026!2.90e-16!145;UBERON:0001041!1.59e-14!87;UBERON:0000161!5.80e-14!36;UBERON:0000072!6.36e-14!47;UBERON:0000166!9.30e-14!22;UBERON:0003124!2.15e-13!7;UBERON:0004921!3.53e-13!118;UBERON:0000165!3.00e-11!29;UBERON:0000930!3.00e-11!29;UBERON:0000478!4.58e-11!24;UBERON:0008947!1.26e-10!38;UBERON:0003258!1.26e-10!38;UBERON:0000974!3.93e-10!10;UBERON:0000153!6.52e-10!62;UBERON:0007811!6.52e-10!62;UBERON:0000365!1.95e-09!5;UBERON:0003102!2.56e-09!99;UBERON:0000064!8.03e-09!218;UBERON:0004923!8.15e-09!66;UBERON:0000344!1.60e-08!20;UBERON:0001987!2.54e-08!4;UBERON:0004340!2.54e-08!4;UBERON:0005910!8.79e-08!6;UBERON:0003729!9.33e-08!13;UBERON:0000033!1.81e-07!56;UBERON:0003343!2.03e-07!4;UBERON:0004785!2.03e-07!4;UBERON:0006562!3.47e-07!11;UBERON:0001444!3.87e-07!49;UBERON:0000305!7.25e-07!7
|ontology_enrichment_uberon=UBERON:0004119!9.24e-25!160;UBERON:0000925!9.24e-25!160;UBERON:0006595!9.24e-25!160;UBERON:0001004!3.81e-23!74;UBERON:0001557!4.86e-20!19;UBERON:0005631!5.40e-18!14;UBERON:0000158!5.40e-18!14;UBERON:0001737!9.49e-18!9;UBERON:0000065!1.13e-16!54;UBERON:0001007!2.90e-16!145;UBERON:0001555!2.90e-16!145;UBERON:0007026!2.90e-16!145;UBERON:0001041!1.59e-14!87;UBERON:0000161!5.80e-14!36;UBERON:0000072!6.36e-14!47;UBERON:0000166!9.30e-14!22;UBERON:0003124!2.15e-13!7;UBERON:0004921!3.53e-13!118;UBERON:0000165!3.00e-11!29;UBERON:0000930!3.00e-11!29;UBERON:0000478!4.58e-11!24;UBERON:0008947!1.26e-10!38;UBERON:0003258!1.26e-10!38;UBERON:0000974!3.93e-10!10;UBERON:0000153!6.52e-10!62;UBERON:0007811!6.52e-10!62;UBERON:0000365!1.95e-09!5;UBERON:0003102!2.56e-09!99;UBERON:0000064!8.03e-09!218;UBERON:0004923!8.15e-09!66;UBERON:0000344!1.60e-08!20;UBERON:0001987!2.54e-08!4;UBERON:0004340!2.54e-08!4;UBERON:0005910!8.79e-08!6;UBERON:0003729!9.33e-08!13;UBERON:0000033!1.81e-07!56;UBERON:0003343!2.03e-07!4;UBERON:0004785!2.03e-07!4;UBERON:0006562!3.47e-07!11;UBERON:0001444!3.87e-07!49;UBERON:0000305!7.25e-07!7
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1613_tongue_Sebocyte_esophagus_amniotic_throat_Prostate_Urothelial



Phase1 CAGE Peaks

Hg19::chr11:119982702..119982714,-p@chr11:119982702..119982714
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Hg19::chr11:119982790..119982805,-p@chr11:119982790..119982805
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Hg19::chr11:119982836..119982847,-p@chr11:119982836..119982847
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Hg19::chr11:119986113..119986126,-p1@BX648072
Hg19::chr11:120008074..120008088,-p13@TRIM29


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.24e-25160
endoderm9.24e-25160
presumptive endoderm9.24e-25160
respiratory system3.81e-2374
upper respiratory tract4.86e-2019
extraembryonic membrane5.40e-1814
membranous layer5.40e-1814
larynx9.49e-189
respiratory tract1.13e-1654
digestive system2.90e-16145
digestive tract2.90e-16145
primitive gut2.90e-16145
foregut1.59e-1487
orifice5.80e-1436
segment of respiratory tract6.36e-1447
oral opening9.30e-1422
chorion2.15e-137
subdivision of digestive tract3.53e-13118
mouth3.00e-1129
stomodeum3.00e-1129
extraembryonic structure4.58e-1124
respiratory primordium1.26e-1038
endoderm of foregut1.26e-1038
neck3.93e-1010
anterior region of body6.52e-1062
craniocervical region6.52e-1062
urothelium1.95e-095
surface structure2.56e-0999
organ part8.03e-09218
organ component layer8.15e-0966
mucosa1.60e-0820
placenta2.54e-084
allantois2.54e-084
transitional epithelium8.79e-086
mouth mucosa9.33e-0813
head1.81e-0756
mucosa of oral region2.03e-074
respiratory system mucosa2.03e-074
pharynx3.47e-0711
subdivision of head3.87e-0749
amnion7.25e-077
Disease
Ontology termp-valuen
carcinoma7.03e-09106
squamous cell carcinoma6.44e-0714


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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