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Coexpression cluster:C2401: Difference between revisions

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|ontology_enrichment_disease=DOID:305!5.20e-11!106;DOID:299!5.03e-10!25
|ontology_enrichment_disease=DOID:305!5.20e-11!106;DOID:299!5.03e-10!25
|ontology_enrichment_uberon=UBERON:0001008!3.20e-25!45;UBERON:0006554!1.88e-24!44;UBERON:0005172!1.06e-23!55;UBERON:0005173!1.06e-23!55;UBERON:0002113!1.45e-21!27;UBERON:0003918!1.45e-21!27;UBERON:0005095!1.45e-21!27;UBERON:0007687!1.45e-21!27;UBERON:0002417!5.38e-21!61;UBERON:0000916!5.38e-21!61;UBERON:0000489!1.25e-19!32;UBERON:0000058!3.01e-19!26;UBERON:0000080!5.29e-18!18;UBERON:0002120!5.29e-18!18;UBERON:0004875!5.29e-18!18;UBERON:0005721!5.29e-18!18;UBERON:0005754!5.29e-18!18;UBERON:0007297!5.29e-18!18;UBERON:0006555!3.87e-17!17;UBERON:0005103!3.87e-17!17;UBERON:0000083!3.87e-17!17;UBERON:0009201!3.87e-17!17;UBERON:0004819!3.87e-17!17;UBERON:0006553!3.87e-17!17;UBERON:0003074!3.87e-17!17;UBERON:0003060!3.87e-17!17;UBERON:0003887!4.03e-16!21;UBERON:0005177!4.37e-16!107;UBERON:0004211!4.45e-16!16;UBERON:0001285!4.45e-16!16;UBERON:0007684!4.45e-16!16;UBERON:0003220!4.45e-16!16;UBERON:0004208!4.45e-16!16;UBERON:0004876!1.51e-15!20;UBERON:0003064!2.72e-15!37;UBERON:0004119!8.71e-15!169;UBERON:0000925!8.71e-15!169;UBERON:0006595!8.71e-15!169;UBERON:0004921!1.55e-14!129;UBERON:0004185!1.55e-14!129;UBERON:0000466!3.06e-13!126;UBERON:0001225!1.51e-12!13;UBERON:0008987!1.51e-12!13;UBERON:0009569!1.86e-12!113;UBERON:0009773!3.00e-12!12;UBERON:0001231!3.00e-12!12;UBERON:0004810!3.00e-12!12;UBERON:0001007!2.29e-11!155;UBERON:0001555!2.29e-11!155;UBERON:0007026!2.29e-11!155;UBERON:0000077!3.09e-11!130;UBERON:0003886!8.32e-11!63;UBERON:0001851!9.61e-11!16;UBERON:0003104!1.46e-10!238;UBERON:0009142!1.46e-10!238;UBERON:0000353!4.59e-10!17;UBERON:0005911!2.97e-09!82;UBERON:0009497!3.02e-09!25;UBERON:0000015!3.02e-09!25;UBERON:0002423!3.02e-09!25;UBERON:0006235!3.02e-09!25;UBERON:0004161!3.02e-09!25;UBERON:0009856!5.47e-09!26;UBERON:0001737!9.48e-09!9;UBERON:0002553!1.00e-08!70;UBERON:0007499!3.10e-08!25;UBERON:0000074!3.21e-08!7;UBERON:0001229!3.21e-08!7;UBERON:0001230!3.21e-08!7;UBERON:0005749!3.21e-08!7;UBERON:0004199!3.21e-08!7;UBERON:0004209!3.21e-08!7;UBERON:0004198!3.21e-08!7;UBERON:0000464!3.67e-08!104;UBERON:0009854!4.54e-08!23;UBERON:0005409!6.51e-08!35;UBERON:0000062!1.11e-07!511;UBERON:0001041!1.24e-07!98;UBERON:0008835!2.55e-07!22;UBERON:0003894!2.55e-07!22;UBERON:0003929!6.65e-07!54
|ontology_enrichment_uberon=UBERON:0001008!3.20e-25!45;UBERON:0006554!1.88e-24!44;UBERON:0005172!1.06e-23!55;UBERON:0005173!1.06e-23!55;UBERON:0002113!1.45e-21!27;UBERON:0003918!1.45e-21!27;UBERON:0005095!1.45e-21!27;UBERON:0007687!1.45e-21!27;UBERON:0002417!5.38e-21!61;UBERON:0000916!5.38e-21!61;UBERON:0000489!1.25e-19!32;UBERON:0000058!3.01e-19!26;UBERON:0000080!5.29e-18!18;UBERON:0002120!5.29e-18!18;UBERON:0004875!5.29e-18!18;UBERON:0005721!5.29e-18!18;UBERON:0005754!5.29e-18!18;UBERON:0007297!5.29e-18!18;UBERON:0006555!3.87e-17!17;UBERON:0005103!3.87e-17!17;UBERON:0000083!3.87e-17!17;UBERON:0009201!3.87e-17!17;UBERON:0004819!3.87e-17!17;UBERON:0006553!3.87e-17!17;UBERON:0003074!3.87e-17!17;UBERON:0003060!3.87e-17!17;UBERON:0003887!4.03e-16!21;UBERON:0005177!4.37e-16!107;UBERON:0004211!4.45e-16!16;UBERON:0001285!4.45e-16!16;UBERON:0007684!4.45e-16!16;UBERON:0003220!4.45e-16!16;UBERON:0004208!4.45e-16!16;UBERON:0004876!1.51e-15!20;UBERON:0003064!2.72e-15!37;UBERON:0004119!8.71e-15!169;UBERON:0000925!8.71e-15!169;UBERON:0006595!8.71e-15!169;UBERON:0004921!1.55e-14!129;UBERON:0004185!1.55e-14!129;UBERON:0000466!3.06e-13!126;UBERON:0001225!1.51e-12!13;UBERON:0008987!1.51e-12!13;UBERON:0009569!1.86e-12!113;UBERON:0009773!3.00e-12!12;UBERON:0001231!3.00e-12!12;UBERON:0004810!3.00e-12!12;UBERON:0001007!2.29e-11!155;UBERON:0001555!2.29e-11!155;UBERON:0007026!2.29e-11!155;UBERON:0000077!3.09e-11!130;UBERON:0003886!8.32e-11!63;UBERON:0001851!9.61e-11!16;UBERON:0003104!1.46e-10!238;UBERON:0009142!1.46e-10!238;UBERON:0000353!4.59e-10!17;UBERON:0005911!2.97e-09!82;UBERON:0009497!3.02e-09!25;UBERON:0000015!3.02e-09!25;UBERON:0002423!3.02e-09!25;UBERON:0006235!3.02e-09!25;UBERON:0004161!3.02e-09!25;UBERON:0009856!5.47e-09!26;UBERON:0001737!9.48e-09!9;UBERON:0002553!1.00e-08!70;UBERON:0007499!3.10e-08!25;UBERON:0000074!3.21e-08!7;UBERON:0001229!3.21e-08!7;UBERON:0001230!3.21e-08!7;UBERON:0005749!3.21e-08!7;UBERON:0004199!3.21e-08!7;UBERON:0004209!3.21e-08!7;UBERON:0004198!3.21e-08!7;UBERON:0000464!3.67e-08!104;UBERON:0009854!4.54e-08!23;UBERON:0005409!6.51e-08!35;UBERON:0000062!1.11e-07!511;UBERON:0001041!1.24e-07!98;UBERON:0008835!2.55e-07!22;UBERON:0003894!2.55e-07!22;UBERON:0003929!6.65e-07!54
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296208246865904!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.039068050020371!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293035654666945
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}}
}}

Revision as of 11:33, 5 September 2012


Full id: C2401_serous_Renal_renal_signet_mesothelioma_kidney_clear



Phase1 CAGE Peaks

Hg19::chr17:36065029..36065045,-p@chr17:36065029..36065045
-
Hg19::chr17:36105042..36105060,-p1@HNF1B
Hg19::chr17:36105163..36105191,+p1@ENST00000558143
Hg19::chr18:3456189..3456200,+p@chr18:3456189..3456200
+


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:0001822kidney development0.0276698457553279
GO:0001655urogenital system development0.0276698457553279



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
renal system3.20e-2545
urinary system structure1.88e-2444
abdomen element1.06e-2355
abdominal segment element1.06e-2355
kidney1.45e-2127
kidney mesenchyme1.45e-2127
kidney rudiment1.45e-2127
kidney field1.45e-2127
abdominal segment of trunk5.38e-2161
abdomen5.38e-2161
cavitated compound organ1.25e-1932
duct3.01e-1926
mesonephros5.29e-1818
pronephros5.29e-1818
nephrogenic cord5.29e-1818
pronephric mesoderm5.29e-1818
rostral part of nephrogenic cord5.29e-1818
presumptive pronephric mesoderm5.29e-1818
excretory tube3.87e-1717
mesonephric epithelium3.87e-1717
mesonephric tubule3.87e-1717
nephric duct3.87e-1717
kidney epithelium3.87e-1717
renal duct3.87e-1717
mesonephric duct3.87e-1717
pronephric duct3.87e-1717
intraembryonic coelom4.03e-1621
trunk region element4.37e-16107
nephron epithelium4.45e-1616
nephron4.45e-1616
uriniferous tubule4.45e-1616
metanephric mesenchyme4.45e-1616
nephrogenic mesenchyme4.45e-1616
urogenital ridge1.51e-1520
intermediate mesoderm2.72e-1537
endoderm-derived structure8.71e-15169
endoderm8.71e-15169
presumptive endoderm8.71e-15169
subdivision of digestive tract1.55e-14129
endodermal part of digestive tract1.55e-14129
immaterial anatomical entity3.06e-13126
cortex of kidney1.51e-1213
renal parenchyma1.51e-1213
subdivision of trunk1.86e-12113
renal tubule3.00e-1212
nephron tubule3.00e-1212
nephron tubule epithelium3.00e-1212
digestive system2.29e-11155
digestive tract2.29e-11155
primitive gut2.29e-11155
mixed endoderm/mesoderm-derived structure3.09e-11130
body cavity precursor8.32e-1163
cortex9.61e-1116
mesenchyme1.46e-10238
entire embryonic mesenchyme1.46e-10238
parenchyma4.59e-1017
endo-epithelium2.97e-0982
epithelium of foregut-midgut junction3.02e-0925
anatomical boundary3.02e-0925
hepatobiliary system3.02e-0925
foregut-midgut junction3.02e-0925
septum transversum3.02e-0925
sac5.47e-0926
larynx9.48e-099
anatomical cavity1.00e-0870
epithelial sac3.10e-0825
renal glomerulus3.21e-087
renal corpuscle3.21e-087
glomerular capsule3.21e-087
glomerular tuft3.21e-087
S-shaped body3.21e-087
renal vesicle3.21e-087
comma-shaped body3.21e-087
anatomical space3.67e-08104
digestive tract diverticulum4.54e-0823
gastrointestinal system6.51e-0835
organ1.11e-07511
foregut1.24e-0798
hepatic diverticulum2.55e-0722
liver primordium2.55e-0722
gut epithelium6.65e-0754
Disease
Ontology termp-valuen
carcinoma5.20e-11106
adenocarcinoma5.03e-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)

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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

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

TF#promotersEnrichmentp-valueq-value
BCL11A#53335214.18472755180350.007108328585298740.0296208246865904
HNF4A#3172211.56614518147680.01057585681762490.039068050020371
HNF4G#3174214.37671126322340.006924169980439180.0293035654666945



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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