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Coexpression cluster:C1607: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;2:10.8946065428824:0.012515829121883:0.0452767813529735
|tf_chipseq_enrich=GATA3#2625;2:10.8946065428824:0.012515829121883:0.0452767813529735
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}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1607_seminal_ductus_Hepatocyte_epididymis_pancreas_kidney_stomach



Phase1 CAGE Peaks

Hg19::chr11:111170526..111170544,-p3@C11orf92
Hg19::chr11:111852954..111852989,+p7@DIXDC1
Hg19::chr12:18414395..18414406,+p3@PIK3C2G
Hg19::chr19:14172840..14172853,-p@chr19:14172840..14172853
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Hg19::chr19:14172854..14172901,-p@chr19:14172854..14172901
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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:0035005phosphatidylinositol-4-phosphate 3-kinase activity0.0105966502627415
GO:0035004phosphoinositide 3-kinase activity0.0131152207783198
GO:00163031-phosphatidylinositol-3-kinase activity0.0131152207783198
GO:0005942phosphoinositide 3-kinase complex0.0131152207783198
GO:0016307phosphatidylinositol phosphate kinase activity0.0131152207783198
GO:0046854phosphoinositide phosphorylation0.0131152207783198
GO:0046834lipid phosphorylation0.0131152207783198
GO:0001727lipid kinase activity0.0167693862056444
GO:0030258lipid modification0.020393644455001
GO:0004428inositol or phosphatidylinositol kinase activity0.0232910130371656
GO:0030384phosphoinositide metabolic process0.0256597345886452
GO:0006650glycerophospholipid metabolic process0.0296866077337913
GO:0048015phosphoinositide-mediated signaling0.0349854547671642
GO:0016055Wnt receptor signaling pathway0.0365072107407221
GO:0044445cytosolic part0.044618264677261
GO:0006644phospholipid metabolic process0.0473160554453427



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
chorionic membrane mesenchymal stem cell7.97e-093
endodermal cell4.26e-0758


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
GATA3#2625210.89460654288240.0125158291218830.0452767813529735



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.