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Coexpression cluster:C631: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;7:4.4532334232845:0.000375585717003615:0.00373188057255642
|tf_chipseq_enrich=EBF1#1879;7:4.4532334232845:0.000375585717003615:0.00373188057255642
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}}
}}

Revision as of 14:21, 26 November 2012


Full id: C631_b_plasma_xeroderma_lymphoma_splenic_Burkitt_B



Phase1 CAGE Peaks

Hg19::chr15:31521567..31521649,-p1@ENST00000558109
p1@ENST00000559853
p1@ENST00000560812
Hg19::chr18:10890571..10890584,-p1@PIEZO2
Hg19::chr18:4264542..4264555,+p6@LOC284215
Hg19::chr3:178261188..178261195,-p@chr3:178261188..178261195
-
Hg19::chr3:189838731..189838748,+p1@LEPREL1-AS1
Hg19::chr3:98255434..98255449,-p@chr3:98255434..98255449
-
Hg19::chr7:114556667..114556679,+p@chr7:114556667..114556679
+
Hg19::chr7:119999940..119999943,+p@chr7:119999940..119999943
+
Hg19::chr8:135577784..135577795,-p15@ZFAT
Hg19::chr8:135577814..135577826,-p12@ZFAT
Hg19::chr8:135577829..135577861,-p6@ZFAT
Hg19::chr8:135577914..135577919,-p23@ZFAT
Hg19::chrX:11682587..11682597,-p25@ARHGAP6
Hg19::chrX:11778510..11778522,+p19@MSL3


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:0005100Rho GTPase activator activity0.0137662388633777
GO:0005884actin filament0.0137662388633777
GO:0030041actin filament polymerization0.0137662388633777
GO:0005070SH3/SH2 adaptor activity0.0137662388633777
GO:0060090molecular adaptor activity0.0137662388633777
GO:0008154actin polymerization and/or depolymerization0.0137662388633777
GO:0030674protein binding, bridging0.0164179324149299
GO:0051258protein polymerization0.0164179324149299
GO:0005099Ras GTPase activator activity0.0248243651634679
GO:0007266Rho protein signal transduction0.0254562580949017
GO:0030036actin cytoskeleton organization and biogenesis0.0293378861022803
GO:0030029actin filament-based process0.0293378861022803
GO:0015629actin cytoskeleton0.0308308199512721
GO:0005096GTPase activator activity0.0336579704294293
GO:0007265Ras protein signal transduction0.0376746247774984
GO:0008047enzyme activator activity0.0376746247774984
GO:0005083small GTPase regulator activity0.0376746247774984
GO:0007010cytoskeleton organization and biogenesis0.0498862840605576
GO:0030695GTPase regulator activity0.0498862840605576



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>


Disease
Ontology termp-valuen
genetic disease1.30e-191
monogenic disease1.30e-191
xeroderma pigmentosum1.30e-191
lymphoma3.14e-0810


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
EBF1#187974.45323342328450.0003755857170036150.00373188057255642



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.