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Coexpression cluster:C2177: Difference between revisions

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|pathway_enrichment=1.34994904617325e-07;8.54517746227668e-05;2;11;{HSP90B1,11} (Static Module):NA
|pathway_enrichment=1.34994904617325e-07;8.54517746227668e-05;2;11;{HSP90B1,11} (Static Module):NA
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}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2177_Hepatocyte_testicular_smallcell_thyroid_Smooth_mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:104337515..104337541,+p3@HSP90B1
Hg19::chr15:99797845..99797875,+p1@HSP90B2P
Hg19::chr15:99798553..99798559,+p2@HSP90B2P
Hg19::chr15:99799810..99799835,+p@chr15:99799810..99799835
+


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


p.valueFDRnGenesnPathwayName
1.34994904617325e-078.54517746227668e-05211{HSP90B1,11} (Static Module):NA



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:0051082unfolded protein binding0.00358663320311547
GO:0006457protein folding0.00534750789630332
GO:0046790virion binding0.0102038813464514
GO:0050750low-density lipoprotein receptor binding0.0113687003422083
GO:0051208sequestering of calcium ion0.0113687003422083
GO:0005783endoplasmic reticulum0.0113687003422083
GO:0051238sequestering of metal ion0.0113687003422083
GO:0006950response to stress0.0168074092660392
GO:0051235maintenance of localization0.027875829922043
GO:0001666response to hypoxia0.0293685782503145
GO:0005788endoplasmic reticulum lumen0.0326240636776248
GO:0048471perinuclear region of cytoplasm0.0326240636776248
GO:0048770pigment granule0.0362549912429353
GO:0042470melanosome0.0362549912429353
GO:0055074calcium ion homeostasis0.0417632496534629
GO:0006874cellular calcium ion homeostasis0.0417632496534629
GO:0006875cellular metal ion homeostasis0.0417632496534629
GO:0055065metal ion homeostasis0.0417632496534629
GO:0005792microsome0.0485848139057113
GO:0042598vesicular fraction0.0485848139057113
GO:0006916anti-apoptosis0.0485848139057113
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0485848139057113
GO:0055066di-, tri-valent inorganic cation homeostasis0.0485848139057113
GO:0030003cellular cation homeostasis0.0495684243571312
GO:0055080cation homeostasis0.0495684243571312
GO:0043066negative regulation of apoptosis0.0498633436779434
GO:0043069negative regulation of programmed cell death0.0498633436779434
GO:0055082cellular chemical homeostasis0.0498633436779434
GO:0006873cellular ion homeostasis0.0498633436779434



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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
reproductive structure6.70e-0859
reproductive system6.70e-0859
Disease
Ontology termp-valuen
disease of cellular proliferation5.94e-17239
cancer4.51e-16235
cell type cancer2.17e-10143
carcinoma5.45e-09106
reproductive organ cancer2.05e-0829
ovarian cancer3.65e-0814
female reproductive organ cancer5.14e-0827


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


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.