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Coexpression cluster:C2891: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001008!5.37e-19!45;UBERON:0006554!1.64e-18!44;UBERON:0003064!1.63e-12!37;UBERON:0000489!1.97e-10!32;UBERON:0002113!2.72e-10!27;UBERON:0003918!2.72e-10!27;UBERON:0005095!2.72e-10!27;UBERON:0007687!2.72e-10!27;UBERON:0000080!1.57e-08!18;UBERON:0002120!1.57e-08!18;UBERON:0004875!1.57e-08!18;UBERON:0005721!1.57e-08!18;UBERON:0005754!1.57e-08!18;UBERON:0007297!1.57e-08!18;UBERON:0005156!1.84e-08!59;UBERON:0000990!1.84e-08!59;UBERON:0004876!2.77e-08!20;UBERON:0000162!4.67e-08!14;UBERON:0001353!4.67e-08!14;UBERON:0000163!4.67e-08!14;UBERON:0006866!4.67e-08!14;UBERON:0000164!4.67e-08!14;UBERON:0000931!4.67e-08!14;UBERON:0006555!5.46e-08!17;UBERON:0005103!5.46e-08!17;UBERON:0000083!5.46e-08!17;UBERON:0009201!5.46e-08!17;UBERON:0004819!5.46e-08!17;UBERON:0006553!5.46e-08!17;UBERON:0003074!5.46e-08!17;UBERON:0003060!5.46e-08!17;UBERON:0001046!1.36e-07!19;UBERON:0004211!2.10e-07!16;UBERON:0001285!2.10e-07!16;UBERON:0007684!2.10e-07!16;UBERON:0003220!2.10e-07!16;UBERON:0004208!2.10e-07!16;UBERON:0003101!2.60e-07!22;UBERON:0000079!2.60e-07!22;UBERON:0004122!3.60e-07!15;UBERON:0009773!4.64e-07!12;UBERON:0001231!4.64e-07!12;UBERON:0004810!4.64e-07!12;UBERON:0003937!8.54e-07!12;UBERON:0005399!8.54e-07!12
|ontology_enrichment_uberon=UBERON:0001008!5.37e-19!45;UBERON:0006554!1.64e-18!44;UBERON:0003064!1.63e-12!37;UBERON:0000489!1.97e-10!32;UBERON:0002113!2.72e-10!27;UBERON:0003918!2.72e-10!27;UBERON:0005095!2.72e-10!27;UBERON:0007687!2.72e-10!27;UBERON:0000080!1.57e-08!18;UBERON:0002120!1.57e-08!18;UBERON:0004875!1.57e-08!18;UBERON:0005721!1.57e-08!18;UBERON:0005754!1.57e-08!18;UBERON:0007297!1.57e-08!18;UBERON:0005156!1.84e-08!59;UBERON:0000990!1.84e-08!59;UBERON:0004876!2.77e-08!20;UBERON:0000162!4.67e-08!14;UBERON:0001353!4.67e-08!14;UBERON:0000163!4.67e-08!14;UBERON:0006866!4.67e-08!14;UBERON:0000164!4.67e-08!14;UBERON:0000931!4.67e-08!14;UBERON:0006555!5.46e-08!17;UBERON:0005103!5.46e-08!17;UBERON:0000083!5.46e-08!17;UBERON:0009201!5.46e-08!17;UBERON:0004819!5.46e-08!17;UBERON:0006553!5.46e-08!17;UBERON:0003074!5.46e-08!17;UBERON:0003060!5.46e-08!17;UBERON:0001046!1.36e-07!19;UBERON:0004211!2.10e-07!16;UBERON:0001285!2.10e-07!16;UBERON:0007684!2.10e-07!16;UBERON:0003220!2.10e-07!16;UBERON:0004208!2.10e-07!16;UBERON:0003101!2.60e-07!22;UBERON:0000079!2.60e-07!22;UBERON:0004122!3.60e-07!15;UBERON:0009773!4.64e-07!12;UBERON:0001231!4.64e-07!12;UBERON:0004810!4.64e-07!12;UBERON:0003937!8.54e-07!12;UBERON:0005399!8.54e-07!12
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268679882944544!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486601304257225!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000242244509820662!SMARCC1#6599;4:43.6633593196315:2.74744977017458e-07:1.40726290606799e-05!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.84428476819571e-06!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024503783228416!USF1#7391;4:6.36149927720796:0.000610501139914083:0.0050910354959667!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000683211836781845
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}}
}}

Revision as of 13:14, 5 September 2012


Full id: C2891_Mesenchymal_uterus_smallcell_small_leiomyoma_cervix_acute



Phase1 CAGE Peaks

Hg19::chr7:27224795..27224840,-p2@HOXA11
Hg19::chr7:27224842..27224872,-p1@HOXA11
Hg19::chr7:27225007..27225030,+p2@HOXA11-AS1
Hg19::chr7:27225038..27225057,+p1@HOXA11-AS1


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:0001759induction of an organ0.00323796067349582
GO:0010092specification of organ identity0.00323796067349582
GO:0045168cell-cell signaling during cell fate commitment0.00323796067349582
GO:0031128induction0.00323796067349582
GO:0001656metanephros development0.00777110561638996
GO:0001822kidney development0.00925131620998805
GO:0001655urogenital system development0.00925131620998805
GO:0045165cell fate commitment0.0143684504886377
GO:0003002regionalization0.0156501432552298
GO:0007389pattern specification process0.0200753561756741
GO:0001501skeletal development0.0307606263982103
GO:0009887organ morphogenesis0.048839240158562



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><br>

Cell Type
Ontology termp-valuen
kidney cell4.17e-0818
kidney epithelial cell4.17e-0818
epithelial cell of nephron2.10e-0716
skin fibroblast2.63e-0723
kidney tubule cell4.64e-0712
nephron tubule epithelial cell4.64e-0712
Uber Anatomy
Ontology termp-valuen
renal system5.37e-1945
urinary system structure1.64e-1844
intermediate mesoderm1.63e-1237
cavitated compound organ1.97e-1032
kidney2.72e-1027
kidney mesenchyme2.72e-1027
kidney rudiment2.72e-1027
kidney field2.72e-1027
mesonephros1.57e-0818
pronephros1.57e-0818
nephrogenic cord1.57e-0818
pronephric mesoderm1.57e-0818
rostral part of nephrogenic cord1.57e-0818
presumptive pronephric mesoderm1.57e-0818
reproductive structure1.84e-0859
reproductive system1.84e-0859
urogenital ridge2.77e-0820
cloaca4.67e-0814
anal region4.67e-0814
embryonic cloaca4.67e-0814
terminal part of digestive tract4.67e-0814
primitive urogenital sinus4.67e-0814
proctodeum4.67e-0814
excretory tube5.46e-0817
mesonephric epithelium5.46e-0817
mesonephric tubule5.46e-0817
nephric duct5.46e-0817
kidney epithelium5.46e-0817
renal duct5.46e-0817
mesonephric duct5.46e-0817
pronephric duct5.46e-0817
hindgut1.36e-0719
nephron epithelium2.10e-0716
nephron2.10e-0716
uriniferous tubule2.10e-0716
metanephric mesenchyme2.10e-0716
nephrogenic mesenchyme2.10e-0716
male organism2.60e-0722
male reproductive system2.60e-0722
genitourinary system3.60e-0715
renal tubule4.64e-0712
nephron tubule4.64e-0712
nephron tubule epithelium4.64e-0712
sex gland8.54e-0712
male reproductive gland8.54e-0712


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
CEBPB#105147.971147625824820.0002476385788090830.00268679882944544
MAX#414946.452555509007120.0005767613195645490.00486601304257225
SMARCB1#6598418.25271578115749.00423392720929e-060.000242244509820662
SMARCC1#6599443.66335931963152.74744977017458e-071.40726290606799e-05
SUZ12#23512450.11578091106291.5827390373096e-078.84428476819571e-06
TBP#690843.706770687096390.005296377814784350.024503783228416
USF1#739146.361499277207960.0006105011399140830.0050910354959667
USF2#7392412.99219738506963.50833029870167e-050.000683211836781845



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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