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Coexpression cluster:C1363: Difference between revisions

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|ontology_enrichment_disease=DOID:299!3.82e-10!25
|ontology_enrichment_disease=DOID:299!3.82e-10!25
|ontology_enrichment_uberon=UBERON:0005172!3.98e-22!55;UBERON:0005173!3.98e-22!55;UBERON:0002417!4.40e-19!61;UBERON:0000916!4.40e-19!61;UBERON:0009497!3.47e-13!25;UBERON:0000015!3.47e-13!25;UBERON:0002423!3.47e-13!25;UBERON:0006235!3.47e-13!25;UBERON:0004161!3.47e-13!25;UBERON:0005409!8.92e-13!35;UBERON:0009854!1.57e-12!23;UBERON:0002113!5.78e-12!27;UBERON:0003918!5.78e-12!27;UBERON:0005095!5.78e-12!27;UBERON:0007687!5.78e-12!27;UBERON:0002368!6.53e-12!35;UBERON:0004921!6.86e-12!129;UBERON:0004185!6.86e-12!129;UBERON:0003929!7.05e-12!54;UBERON:0005177!1.12e-11!107;UBERON:0002107!2.24e-11!19;UBERON:0006925!2.24e-11!19;UBERON:0008836!2.24e-11!19;UBERON:0008835!3.37e-11!22;UBERON:0003894!3.37e-11!22;UBERON:0002530!3.89e-11!59;UBERON:0001007!5.50e-11!155;UBERON:0001555!5.50e-11!155;UBERON:0007026!5.50e-11!155;UBERON:0000949!6.28e-11!45;UBERON:0000466!1.09e-10!126;UBERON:0009856!1.12e-10!26;UBERON:0005057!2.03e-10!26;UBERON:0000160!2.59e-10!27;UBERON:0000080!8.19e-10!18;UBERON:0002120!8.19e-10!18;UBERON:0004875!8.19e-10!18;UBERON:0005721!8.19e-10!18;UBERON:0005754!8.19e-10!18;UBERON:0007297!8.19e-10!18;UBERON:0003887!1.05e-09!21;UBERON:0000489!1.69e-09!32;UBERON:0007499!1.78e-09!25;UBERON:0004119!3.49e-09!169;UBERON:0000925!3.49e-09!169;UBERON:0006595!3.49e-09!169;UBERON:0006554!4.59e-09!44;UBERON:0000059!6.34e-09!11;UBERON:0009569!8.19e-09!113;UBERON:0000058!8.57e-09!26;UBERON:0001008!9.18e-09!45;UBERON:0004876!1.37e-08!20;UBERON:0006555!1.49e-08!17;UBERON:0005103!1.49e-08!17;UBERON:0000083!1.49e-08!17;UBERON:0009201!1.49e-08!17;UBERON:0004819!1.49e-08!17;UBERON:0006553!1.49e-08!17;UBERON:0003074!1.49e-08!17;UBERON:0003060!1.49e-08!17;UBERON:0002365!1.96e-08!31;UBERON:0002330!1.96e-08!31;UBERON:0009773!3.37e-08!12;UBERON:0001231!3.37e-08!12;UBERON:0004810!3.37e-08!12;UBERON:0005911!3.46e-08!82;UBERON:0000077!1.42e-07!130;UBERON:0004211!2.78e-07!16;UBERON:0001285!2.78e-07!16;UBERON:0007684!2.78e-07!16;UBERON:0003220!2.78e-07!16;UBERON:0004208!2.78e-07!16;UBERON:0004907!3.98e-07!5;UBERON:0002553!4.03e-07!70
|ontology_enrichment_uberon=UBERON:0005172!3.98e-22!55;UBERON:0005173!3.98e-22!55;UBERON:0002417!4.40e-19!61;UBERON:0000916!4.40e-19!61;UBERON:0009497!3.47e-13!25;UBERON:0000015!3.47e-13!25;UBERON:0002423!3.47e-13!25;UBERON:0006235!3.47e-13!25;UBERON:0004161!3.47e-13!25;UBERON:0005409!8.92e-13!35;UBERON:0009854!1.57e-12!23;UBERON:0002113!5.78e-12!27;UBERON:0003918!5.78e-12!27;UBERON:0005095!5.78e-12!27;UBERON:0007687!5.78e-12!27;UBERON:0002368!6.53e-12!35;UBERON:0004921!6.86e-12!129;UBERON:0004185!6.86e-12!129;UBERON:0003929!7.05e-12!54;UBERON:0005177!1.12e-11!107;UBERON:0002107!2.24e-11!19;UBERON:0006925!2.24e-11!19;UBERON:0008836!2.24e-11!19;UBERON:0008835!3.37e-11!22;UBERON:0003894!3.37e-11!22;UBERON:0002530!3.89e-11!59;UBERON:0001007!5.50e-11!155;UBERON:0001555!5.50e-11!155;UBERON:0007026!5.50e-11!155;UBERON:0000949!6.28e-11!45;UBERON:0000466!1.09e-10!126;UBERON:0009856!1.12e-10!26;UBERON:0005057!2.03e-10!26;UBERON:0000160!2.59e-10!27;UBERON:0000080!8.19e-10!18;UBERON:0002120!8.19e-10!18;UBERON:0004875!8.19e-10!18;UBERON:0005721!8.19e-10!18;UBERON:0005754!8.19e-10!18;UBERON:0007297!8.19e-10!18;UBERON:0003887!1.05e-09!21;UBERON:0000489!1.69e-09!32;UBERON:0007499!1.78e-09!25;UBERON:0004119!3.49e-09!169;UBERON:0000925!3.49e-09!169;UBERON:0006595!3.49e-09!169;UBERON:0006554!4.59e-09!44;UBERON:0000059!6.34e-09!11;UBERON:0009569!8.19e-09!113;UBERON:0000058!8.57e-09!26;UBERON:0001008!9.18e-09!45;UBERON:0004876!1.37e-08!20;UBERON:0006555!1.49e-08!17;UBERON:0005103!1.49e-08!17;UBERON:0000083!1.49e-08!17;UBERON:0009201!1.49e-08!17;UBERON:0004819!1.49e-08!17;UBERON:0006553!1.49e-08!17;UBERON:0003074!1.49e-08!17;UBERON:0003060!1.49e-08!17;UBERON:0002365!1.96e-08!31;UBERON:0002330!1.96e-08!31;UBERON:0009773!3.37e-08!12;UBERON:0001231!3.37e-08!12;UBERON:0004810!3.37e-08!12;UBERON:0005911!3.46e-08!82;UBERON:0000077!1.42e-07!130;UBERON:0004211!2.78e-07!16;UBERON:0001285!2.78e-07!16;UBERON:0007684!2.78e-07!16;UBERON:0003220!2.78e-07!16;UBERON:0004208!2.78e-07!16;UBERON:0004907!3.98e-07!5;UBERON:0002553!4.03e-07!70
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}}
}}

Revision as of 13:14, 5 September 2012


Full id: C1363_pancreas_small_gall_temporal_duodenum_colon_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr12:56624532..56624554,+p2@SLC39A5
Hg19::chr16:3704849..3704860,+p4@DNASE1
Hg19::chr17:202392..202413,+p1@AK125265
Hg19::chr21:37091670..37091681,+p@chr21:37091670..37091681
+
Hg19::chr22:37975952..37975968,-p2@LGALS2
Hg19::chr2:79384252..79384270,-p@chr2:79384252..79384270
-


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:0004530deoxyribonuclease I activity0.0116566584245849



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
metabolising cell2.34e-1012
endopolyploid cell2.34e-1012
parenchymal cell2.34e-1012
polyploid cell2.34e-1012
hepatocyte2.34e-1012
kidney cell9.42e-1018
kidney epithelial cell9.42e-1018
kidney tubule cell3.37e-0812
nephron tubule epithelial cell3.37e-0812
epithelial cell of nephron2.78e-0716
Uber Anatomy
Ontology termp-valuen
abdomen element3.98e-2255
abdominal segment element3.98e-2255
abdominal segment of trunk4.40e-1961
abdomen4.40e-1961
epithelium of foregut-midgut junction3.47e-1325
anatomical boundary3.47e-1325
hepatobiliary system3.47e-1325
foregut-midgut junction3.47e-1325
septum transversum3.47e-1325
gastrointestinal system8.92e-1335
digestive tract diverticulum1.57e-1223
kidney5.78e-1227
kidney mesenchyme5.78e-1227
kidney rudiment5.78e-1227
kidney field5.78e-1227
endocrine gland6.53e-1235
subdivision of digestive tract6.86e-12129
endodermal part of digestive tract6.86e-12129
gut epithelium7.05e-1254
trunk region element1.12e-11107
liver2.24e-1119
digestive gland2.24e-1119
liver bud2.24e-1119
hepatic diverticulum3.37e-1122
liver primordium3.37e-1122
gland3.89e-1159
digestive system5.50e-11155
digestive tract5.50e-11155
primitive gut5.50e-11155
endocrine system6.28e-1145
immaterial anatomical entity1.09e-10126
sac1.12e-1026
immune organ2.03e-1026
intestine2.59e-1027
mesonephros8.19e-1018
pronephros8.19e-1018
nephrogenic cord8.19e-1018
pronephric mesoderm8.19e-1018
rostral part of nephrogenic cord8.19e-1018
presumptive pronephric mesoderm8.19e-1018
intraembryonic coelom1.05e-0921
cavitated compound organ1.69e-0932
epithelial sac1.78e-0925
endoderm-derived structure3.49e-09169
endoderm3.49e-09169
presumptive endoderm3.49e-09169
urinary system structure4.59e-0944
large intestine6.34e-0911
subdivision of trunk8.19e-09113
duct8.57e-0926
renal system9.18e-0945
urogenital ridge1.37e-0820
excretory tube1.49e-0817
mesonephric epithelium1.49e-0817
mesonephric tubule1.49e-0817
nephric duct1.49e-0817
kidney epithelium1.49e-0817
renal duct1.49e-0817
mesonephric duct1.49e-0817
pronephric duct1.49e-0817
exocrine gland1.96e-0831
exocrine system1.96e-0831
renal tubule3.37e-0812
nephron tubule3.37e-0812
nephron tubule epithelium3.37e-0812
endo-epithelium3.46e-0882
mixed endoderm/mesoderm-derived structure1.42e-07130
nephron epithelium2.78e-0716
nephron2.78e-0716
uriniferous tubule2.78e-0716
metanephric mesenchyme2.78e-0716
nephrogenic mesenchyme2.78e-0716
lower digestive tract3.98e-075
anatomical cavity4.03e-0770
Disease
Ontology termp-valuen
adenocarcinoma3.82e-1025


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ESRRA#2101180.6400523560210.01233705312615740.0447012729476392
HNF4G#3174419.16894835096452.07234608447467e-050.000458157816927286



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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