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Coexpression cluster:C4518: Difference between revisions

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|full_id=C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal
|full_id=C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal
|id=C4518
|id=C4518
|ontology_enrichment_celltype=CL:1000497!2.78e-08!18;CL:0002518!2.78e-08!18;CL:1000507!2.40e-07!12;CL:1000494!2.40e-07!12;CL:0002076!7.73e-07!43;CL:1000449!9.34e-07!16
|ontology_enrichment_celltype=CL:1000507!4.04e-15!10;CL:1000494!4.04e-15!10;CL:1000497!1.29e-13!17;CL:0002518!1.29e-13!17;CL:1000449!4.60e-11!15;CL:0000066!9.83e-08!253;CL:0002681!2.21e-07!12;CL:0002584!2.21e-07!12;CL:0000223!5.50e-07!58;CL:0002076!7.20e-07!42
|ontology_enrichment_disease=DOID:120!3.24e-12!27;DOID:193!1.03e-10!29;DOID:2394!4.57e-10!14
|ontology_enrichment_disease=DOID:120!1.87e-13!27;DOID:193!3.95e-12!29;DOID:2394!3.37e-10!14
|ontology_enrichment_uberon=UBERON:0003133!5.60e-13!48;UBERON:0005156!1.40e-12!59;UBERON:0000990!1.40e-12!59;UBERON:0003100!7.41e-12!41;UBERON:0000489!1.33e-11!32;UBERON:0003134!7.66e-11!37;UBERON:0000474!7.66e-11!37;UBERON:0001008!1.12e-10!45;UBERON:0002113!1.93e-10!27;UBERON:0003918!1.93e-10!27;UBERON:0005095!1.93e-10!27;UBERON:0007687!1.93e-10!27;UBERON:0006554!3.54e-10!44;UBERON:0004876!2.36e-09!20;UBERON:0000475!2.74e-09!365;UBERON:0003886!1.15e-08!63;UBERON:0000058!2.52e-08!26;UBERON:0000080!4.73e-08!18;UBERON:0002120!4.73e-08!18;UBERON:0004875!4.73e-08!18;UBERON:0005721!4.73e-08!18;UBERON:0005754!4.73e-08!18;UBERON:0007297!4.73e-08!18;UBERON:0000464!5.67e-08!104;UBERON:0002553!9.68e-08!70;UBERON:0000992!1.41e-07!13;UBERON:0000922!1.42e-07!612;UBERON:0000991!1.90e-07!21;UBERON:0009196!1.90e-07!21;UBERON:0009117!1.90e-07!21;UBERON:0005564!1.90e-07!21;UBERON:0006555!1.99e-07!17;UBERON:0005103!1.99e-07!17;UBERON:0000083!1.99e-07!17;UBERON:0009201!1.99e-07!17;UBERON:0004819!1.99e-07!17;UBERON:0006553!1.99e-07!17;UBERON:0003074!1.99e-07!17;UBERON:0003060!1.99e-07!17;UBERON:0000481!2.11e-07!347;UBERON:0009773!2.40e-07!12;UBERON:0001231!2.40e-07!12;UBERON:0004810!2.40e-07!12;UBERON:0003064!2.98e-07!37;UBERON:0002050!3.79e-07!605;UBERON:0005423!3.79e-07!605;UBERON:0004175!4.72e-07!25;UBERON:0000468!6.04e-07!659;UBERON:0000923!6.94e-07!604;UBERON:0005291!6.94e-07!604;UBERON:0006598!6.94e-07!604;UBERON:0002532!6.94e-07!604;UBERON:0002100!7.43e-07!216;UBERON:0004176!7.72e-07!22;UBERON:0004211!9.34e-07!16;UBERON:0001285!9.34e-07!16;UBERON:0007684!9.34e-07!16;UBERON:0003220!9.34e-07!16;UBERON:0004208!9.34e-07!16
|ontology_enrichment_uberon=UBERON:0002113!4.43e-17!26;UBERON:0003918!4.43e-17!26;UBERON:0011143!4.43e-17!26;UBERON:0005095!4.43e-17!26;UBERON:0007687!4.43e-17!26;UBERON:0004810!4.04e-15!10;UBERON:0000489!7.70e-15!31;UBERON:0003133!4.59e-13!48;UBERON:0005156!9.70e-13!59;UBERON:0000990!9.70e-13!59;UBERON:0003100!1.75e-12!41;UBERON:0001008!3.97e-12!48;UBERON:0006555!5.34e-12!16;UBERON:0004819!5.34e-12!16;UBERON:0003134!7.76e-12!37;UBERON:0000474!7.76e-12!37;UBERON:0006554!2.58e-11!47;UBERON:0004211!4.60e-11!15;UBERON:0009773!4.60e-11!15;UBERON:0001231!4.60e-11!15;UBERON:0001285!4.60e-11!15;UBERON:0007684!4.60e-11!15;UBERON:0004208!4.60e-11!15;UBERON:0002417!2.94e-09!60;UBERON:0000916!2.94e-09!60;UBERON:0000992!3.01e-09!13;UBERON:0005172!1.95e-08!54;UBERON:0005173!1.95e-08!54;UBERON:0000991!2.22e-08!21;UBERON:0009196!2.22e-08!21;UBERON:0009117!2.22e-08!21;UBERON:0005564!2.22e-08!21;UBERON:0004176!7.69e-08!22;UBERON:0001225!2.21e-07!12;UBERON:0008987!2.21e-07!12;UBERON:0002118!4.77e-07!5;UBERON:0004175!5.42e-07!25
|tf_chipseq_enrich=USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190990777999759
|tf_chipseq_enrich=USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190990777999759
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}}
}}

Revision as of 16:00, 19 October 2012


Full id: C4518_Renal_renal_serous_kidney_Sertoli_mesothelioma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:73109300..73109311,+p5@RGNEF
Hg19::chr5:73109313..73109326,+p4@RGNEF
Hg19::chr5:73109339..73109409,+p2@RGNEF


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
kidney4.43e-1726
kidney mesenchyme4.43e-1726
upper urinary tract4.43e-1726
kidney rudiment4.43e-1726
kidney field4.43e-1726
nephron tubule epithelium4.04e-1510
cavitated compound organ7.70e-1531
reproductive organ4.59e-1348
reproductive structure9.70e-1359
reproductive system9.70e-1359
female organism1.75e-1241
renal system3.97e-1248
excretory tube5.34e-1216
kidney epithelium5.34e-1216
female reproductive organ7.76e-1237
female reproductive system7.76e-1237
urinary system structure2.58e-1147
nephron epithelium4.60e-1115
renal tubule4.60e-1115
nephron tubule4.60e-1115
nephron4.60e-1115
uriniferous tubule4.60e-1115
nephrogenic mesenchyme4.60e-1115
abdominal segment of trunk2.94e-0960
abdomen2.94e-0960
female gonad3.01e-0913
abdomen element1.95e-0854
abdominal segment element1.95e-0854
gonad2.22e-0821
indifferent external genitalia2.22e-0821
indifferent gonad2.22e-0821
gonad primordium2.22e-0821
external genitalia7.69e-0822
cortex of kidney2.21e-0712
renal parenchyma2.21e-0712
right ovary4.77e-075
internal genitalia5.42e-0725
Disease
Ontology termp-valuen
female reproductive organ cancer1.87e-1327
reproductive organ cancer3.95e-1229
ovarian cancer3.37e-1014


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
USF1#739136.361499277207960.00388404057290560.0190990777999759



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4518&oldid=2250858"