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Coexpression cluster:C548: Difference between revisions

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|ontology_enrichment_disease=DOID:120!1.09e-09!27;DOID:193!1.25e-09!29;DOID:299!3.98e-08!25
|ontology_enrichment_disease=DOID:120!1.09e-09!27;DOID:193!1.25e-09!29;DOID:299!3.98e-08!25
|ontology_enrichment_uberon=UBERON:0006555!1.07e-14!17;UBERON:0005103!1.07e-14!17;UBERON:0000083!1.07e-14!17;UBERON:0009201!1.07e-14!17;UBERON:0004819!1.07e-14!17;UBERON:0006553!1.07e-14!17;UBERON:0003074!1.07e-14!17;UBERON:0003060!1.07e-14!17;UBERON:0004211!5.92e-14!16;UBERON:0001285!5.92e-14!16;UBERON:0007684!5.92e-14!16;UBERON:0003220!5.92e-14!16;UBERON:0004208!5.92e-14!16;UBERON:0000080!1.64e-13!18;UBERON:0002120!1.64e-13!18;UBERON:0004875!1.64e-13!18;UBERON:0005721!1.64e-13!18;UBERON:0005754!1.64e-13!18;UBERON:0007297!1.64e-13!18;UBERON:0002113!2.70e-12!27;UBERON:0003918!2.70e-12!27;UBERON:0005095!2.70e-12!27;UBERON:0007687!2.70e-12!27;UBERON:0003887!7.26e-12!21;UBERON:0005172!8.87e-12!55;UBERON:0005173!8.87e-12!55;UBERON:0000466!1.22e-11!126;UBERON:0003886!1.39e-11!63;UBERON:0004876!1.64e-11!20;UBERON:0000058!3.69e-11!26;UBERON:0001225!5.39e-11!13;UBERON:0008987!5.39e-11!13;UBERON:0002417!9.61e-11!61;UBERON:0000916!9.61e-11!61;UBERON:0009773!1.44e-10!12;UBERON:0001231!1.44e-10!12;UBERON:0004810!1.44e-10!12;UBERON:0000489!4.82e-10!32;UBERON:0001851!7.70e-10!16;UBERON:0000464!1.26e-09!104;UBERON:0003103!1.31e-09!69;UBERON:0006554!1.65e-09!44;UBERON:0003064!2.03e-09!37;UBERON:0002553!3.35e-09!70;UBERON:0001008!4.25e-09!45;UBERON:0005177!4.99e-09!107;UBERON:0000353!6.49e-09!17;UBERON:0000483!3.62e-08!309;UBERON:0000119!7.97e-08!312;UBERON:0003914!8.46e-08!118;UBERON:0003929!8.73e-08!54;UBERON:0000074!1.93e-07!7;UBERON:0001229!1.93e-07!7;UBERON:0001230!1.93e-07!7;UBERON:0005749!1.93e-07!7;UBERON:0004199!1.93e-07!7;UBERON:0004209!1.93e-07!7;UBERON:0004198!1.93e-07!7;UBERON:0005156!2.19e-07!59;UBERON:0000990!2.19e-07!59;UBERON:0000062!2.69e-07!511;UBERON:0009569!2.85e-07!113;UBERON:0000481!2.89e-07!347;UBERON:0000064!3.91e-07!219;UBERON:0005911!4.81e-07!82;UBERON:0003133!6.72e-07!48
|ontology_enrichment_uberon=UBERON:0006555!1.07e-14!17;UBERON:0005103!1.07e-14!17;UBERON:0000083!1.07e-14!17;UBERON:0009201!1.07e-14!17;UBERON:0004819!1.07e-14!17;UBERON:0006553!1.07e-14!17;UBERON:0003074!1.07e-14!17;UBERON:0003060!1.07e-14!17;UBERON:0004211!5.92e-14!16;UBERON:0001285!5.92e-14!16;UBERON:0007684!5.92e-14!16;UBERON:0003220!5.92e-14!16;UBERON:0004208!5.92e-14!16;UBERON:0000080!1.64e-13!18;UBERON:0002120!1.64e-13!18;UBERON:0004875!1.64e-13!18;UBERON:0005721!1.64e-13!18;UBERON:0005754!1.64e-13!18;UBERON:0007297!1.64e-13!18;UBERON:0002113!2.70e-12!27;UBERON:0003918!2.70e-12!27;UBERON:0005095!2.70e-12!27;UBERON:0007687!2.70e-12!27;UBERON:0003887!7.26e-12!21;UBERON:0005172!8.87e-12!55;UBERON:0005173!8.87e-12!55;UBERON:0000466!1.22e-11!126;UBERON:0003886!1.39e-11!63;UBERON:0004876!1.64e-11!20;UBERON:0000058!3.69e-11!26;UBERON:0001225!5.39e-11!13;UBERON:0008987!5.39e-11!13;UBERON:0002417!9.61e-11!61;UBERON:0000916!9.61e-11!61;UBERON:0009773!1.44e-10!12;UBERON:0001231!1.44e-10!12;UBERON:0004810!1.44e-10!12;UBERON:0000489!4.82e-10!32;UBERON:0001851!7.70e-10!16;UBERON:0000464!1.26e-09!104;UBERON:0003103!1.31e-09!69;UBERON:0006554!1.65e-09!44;UBERON:0003064!2.03e-09!37;UBERON:0002553!3.35e-09!70;UBERON:0001008!4.25e-09!45;UBERON:0005177!4.99e-09!107;UBERON:0000353!6.49e-09!17;UBERON:0000483!3.62e-08!309;UBERON:0000119!7.97e-08!312;UBERON:0003914!8.46e-08!118;UBERON:0003929!8.73e-08!54;UBERON:0000074!1.93e-07!7;UBERON:0001229!1.93e-07!7;UBERON:0001230!1.93e-07!7;UBERON:0005749!1.93e-07!7;UBERON:0004199!1.93e-07!7;UBERON:0004209!1.93e-07!7;UBERON:0004198!1.93e-07!7;UBERON:0005156!2.19e-07!59;UBERON:0000990!2.19e-07!59;UBERON:0000062!2.69e-07!511;UBERON:0009569!2.85e-07!113;UBERON:0000481!2.89e-07!347;UBERON:0000064!3.91e-07!219;UBERON:0005911!4.81e-07!82;UBERON:0003133!6.72e-07!48
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}}
}}

Revision as of 20:30, 8 August 2012


Full id: C548_Mesothelial_mesenchymal_rhabdomyosarcoma_Renal_mesothelioma_Hepatic_clear



Phase1 CAGE Peaks

Hg19::chr20:6020237..6020248,-p@chr20:6020237..6020248
-
Hg19::chr20:6020266..6020281,-p@chr20:6020266..6020281
-
Hg19::chr20:6020518..6020536,-p@chr20:6020518..6020536
-
Hg19::chr20:6022771..6022780,-p12@LRRN4
Hg19::chr20:6031540..6031548,-p@chr20:6031540..6031548
-
Hg19::chr20:6032946..6032956,-p9@AB527789
Hg19::chr20:6033494..6033509,-p5@AB527789
Hg19::chr20:6033532..6033548,-p2@AB527789
Hg19::chr20:6033667..6033675,-p13@AB527789
Hg19::chr20:6034241..6034256,-p@chr20:6034241..6034256
-
Hg19::chr20:6034557..6034560,-p10@LRRN4
Hg19::chr20:6034576..6034592,-p3@LRRN4
Hg19::chr20:6034598..6034603,-p7@LRRN4
Hg19::chr20:6034607..6034616,-p6@LRRN4
Hg19::chr20:6034618..6034669,-p1@LRRN4
Hg19::chr20:6034672..6034714,-p2@LRRN4
Hg19::chr20:6034828..6034857,-p5@LRRN4


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
excretory tube1.07e-1417
mesonephric epithelium1.07e-1417
mesonephric tubule1.07e-1417
nephric duct1.07e-1417
kidney epithelium1.07e-1417
renal duct1.07e-1417
mesonephric duct1.07e-1417
pronephric duct1.07e-1417
nephron epithelium5.92e-1416
nephron5.92e-1416
uriniferous tubule5.92e-1416
metanephric mesenchyme5.92e-1416
nephrogenic mesenchyme5.92e-1416
mesonephros1.64e-1318
pronephros1.64e-1318
nephrogenic cord1.64e-1318
pronephric mesoderm1.64e-1318
rostral part of nephrogenic cord1.64e-1318
presumptive pronephric mesoderm1.64e-1318
kidney2.70e-1227
kidney mesenchyme2.70e-1227
kidney rudiment2.70e-1227
kidney field2.70e-1227
intraembryonic coelom7.26e-1221
abdomen element8.87e-1255
abdominal segment element8.87e-1255
immaterial anatomical entity1.22e-11126
body cavity precursor1.39e-1163
urogenital ridge1.64e-1120
duct3.69e-1126
cortex of kidney5.39e-1113
renal parenchyma5.39e-1113
abdominal segment of trunk9.61e-1161
abdomen9.61e-1161
renal tubule1.44e-1012
nephron tubule1.44e-1012
nephron tubule epithelium1.44e-1012
cavitated compound organ4.82e-1032
cortex7.70e-1016
anatomical space1.26e-09104
compound organ1.31e-0969
urinary system structure1.65e-0944
intermediate mesoderm2.03e-0937
anatomical cavity3.35e-0970
renal system4.25e-0945
trunk region element4.99e-09107
parenchyma6.49e-0917
epithelium3.62e-08309
cell layer7.97e-08312
epithelial tube8.46e-08118
gut epithelium8.73e-0854
renal glomerulus1.93e-077
renal corpuscle1.93e-077
glomerular capsule1.93e-077
glomerular tuft1.93e-077
S-shaped body1.93e-077
renal vesicle1.93e-077
comma-shaped body1.93e-077
reproductive structure2.19e-0759
reproductive system2.19e-0759
organ2.69e-07511
subdivision of trunk2.85e-07113
multi-tissue structure2.89e-07347
organ part3.91e-07219
endo-epithelium4.81e-0782
reproductive organ6.72e-0748
Disease
Ontology termp-valuen
female reproductive organ cancer1.09e-0927
reproductive organ cancer1.25e-0929
adenocarcinoma3.98e-0825


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.