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Coexpression cluster:C1349: Difference between revisions

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|ontology_enrichment_disease=DOID:305!8.49e-11!106
|ontology_enrichment_disease=DOID:305!8.49e-11!106
|ontology_enrichment_uberon=UBERON:0005911!4.47e-14!82;UBERON:0004119!8.72e-14!169;UBERON:0000925!8.72e-14!169;UBERON:0006595!8.72e-14!169;UBERON:0000058!2.18e-13!26;UBERON:0000464!4.36e-12!104;UBERON:0006554!8.78e-12!44;UBERON:0005631!9.44e-12!14;UBERON:0000158!9.44e-12!14;UBERON:0001008!2.34e-11!45;UBERON:0000065!4.71e-11!53;UBERON:0001004!8.32e-11!72;UBERON:0005178!8.91e-11!34;UBERON:0002224!8.91e-11!34;UBERON:0005153!9.31e-11!37;UBERON:0009773!1.22e-10!12;UBERON:0001231!1.22e-10!12;UBERON:0004810!1.22e-10!12;UBERON:0000466!1.46e-10!126;UBERON:0005181!2.67e-10!35;UBERON:0003064!4.93e-10!37;UBERON:0002048!1.95e-09!22;UBERON:0000117!1.95e-09!22;UBERON:0000171!1.95e-09!22;UBERON:0000170!1.95e-09!22;UBERON:0005597!1.95e-09!22;UBERON:0000118!1.95e-09!22;UBERON:0000064!2.11e-09!219;UBERON:0005177!2.33e-09!107;UBERON:0004876!2.67e-09!20;UBERON:0000080!3.46e-09!18;UBERON:0002120!3.46e-09!18;UBERON:0004875!3.46e-09!18;UBERON:0005721!3.46e-09!18;UBERON:0005754!3.46e-09!18;UBERON:0007297!3.46e-09!18;UBERON:0004211!3.86e-09!16;UBERON:0001285!3.86e-09!16;UBERON:0007684!3.86e-09!16;UBERON:0003220!3.86e-09!16;UBERON:0004208!3.86e-09!16;UBERON:0006555!2.03e-08!17;UBERON:0005103!2.03e-08!17;UBERON:0000083!2.03e-08!17;UBERON:0009201!2.03e-08!17;UBERON:0004819!2.03e-08!17;UBERON:0006553!2.03e-08!17;UBERON:0003074!2.03e-08!17;UBERON:0003060!2.03e-08!17;UBERON:0003124!4.14e-08!7;UBERON:0001007!4.31e-08!155;UBERON:0001555!4.31e-08!155;UBERON:0007026!4.31e-08!155;UBERON:0000077!7.22e-08!130;UBERON:0005157!7.52e-08!51;UBERON:0009569!9.82e-08!113;UBERON:0000365!1.45e-07!5;UBERON:0003887!2.14e-07!21;UBERON:0004807!2.14e-07!28;UBERON:0002294!5.68e-07!7;UBERON:0001173!5.68e-07!7;UBERON:0004912!5.68e-07!7;UBERON:0002113!7.51e-07!27;UBERON:0003918!7.51e-07!27;UBERON:0005095!7.51e-07!27;UBERON:0007687!7.51e-07!27;UBERON:0004923!9.97e-07!57
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}}
}}

Revision as of 17:11, 8 August 2012


Full id: C1349_Alveolar_bile_chorionic_clear_amniotic_papillotubular_serous



Phase1 CAGE Peaks

Hg19::chr11:65778943..65778967,+p2@CST6
Hg19::chr11:65778976..65778988,+p4@CST6
Hg19::chr11:65778994..65779015,+p3@CST6
Hg19::chr11:65779257..65779267,+p6@CST6
Hg19::chr11:65779283..65779289,+p10@CST6
Hg19::chr11:65779378..65779390,+p8@CST6


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
endo-epithelium4.47e-1482
endoderm-derived structure8.72e-14169
endoderm8.72e-14169
presumptive endoderm8.72e-14169
duct2.18e-1326
anatomical space4.36e-12104
urinary system structure8.78e-1244
extraembryonic membrane9.44e-1214
membranous layer9.44e-1214
renal system2.34e-1145
respiratory tract4.71e-1153
respiratory system8.32e-1172
thoracic cavity element8.91e-1134
thoracic cavity8.91e-1134
epithelial bud9.31e-1137
renal tubule1.22e-1012
nephron tubule1.22e-1012
nephron tubule epithelium1.22e-1012
immaterial anatomical entity1.46e-10126
thoracic segment organ2.67e-1035
intermediate mesoderm4.93e-1037
lung1.95e-0922
respiratory tube1.95e-0922
respiration organ1.95e-0922
pair of lungs1.95e-0922
lung primordium1.95e-0922
lung bud1.95e-0922
organ part2.11e-09219
trunk region element2.33e-09107
urogenital ridge2.67e-0920
mesonephros3.46e-0918
pronephros3.46e-0918
nephrogenic cord3.46e-0918
pronephric mesoderm3.46e-0918
rostral part of nephrogenic cord3.46e-0918
presumptive pronephric mesoderm3.46e-0918
nephron epithelium3.86e-0916
nephron3.86e-0916
uriniferous tubule3.86e-0916
metanephric mesenchyme3.86e-0916
nephrogenic mesenchyme3.86e-0916
excretory tube2.03e-0817
mesonephric epithelium2.03e-0817
mesonephric tubule2.03e-0817
nephric duct2.03e-0817
kidney epithelium2.03e-0817
renal duct2.03e-0817
mesonephric duct2.03e-0817
pronephric duct2.03e-0817
chorion4.14e-087
digestive system4.31e-08155
digestive tract4.31e-08155
primitive gut4.31e-08155
mixed endoderm/mesoderm-derived structure7.22e-08130
epithelial fold7.52e-0851
subdivision of trunk9.82e-08113
urothelium1.45e-075
intraembryonic coelom2.14e-0721
respiratory system epithelium2.14e-0728
biliary system5.68e-077
biliary tree5.68e-077
biliary bud5.68e-077
kidney7.51e-0727
kidney mesenchyme7.51e-0727
kidney rudiment7.51e-0727
kidney field7.51e-0727
organ component layer9.97e-0757
Disease
Ontology termp-valuen
carcinoma8.49e-11106


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.