Identifying the genetic variation of gene expression using gene sets: Application of novel gene set eQTL approach to pharmGKB and KEGG

Ryan Abo, Gregory D. Jenkins, Liewei M Wang, Brooke L. Fridley

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Genetic variation underlying the regulation of mRNA gene expression in humans may provide key insights into the molecular mechanisms of human traits and complex diseases. Current statistical methods to map genetic variation associated with mRNA gene expression have typically applied standard linkage and/or association methods; however, when genome-wide SNP and mRNA expression data are available performing all pair wise comparisons is computationally burdensome and may not provide optimal power to detect associations. Consideration of different approaches to account for the high dimensionality and multiple testing issues may provide increased efficiency and statistical power. Here we present a novel approach to model and test the association between genetic variation and mRNA gene expression levels in the context of gene sets (GSs) and pathways, referred to as gene set - expression quantitative trait loci analysis (GS-eQTL). The method uses GSs to initially group SNPs and mRNA expression, followed by the application of principal components analysis (PCA) to collapse the variation and reduce the dimensionality within the GSs. We applied GS-eQTL to assess the association between SNP and mRNA expression level data collected from a cell-based model system using PharmGKB and KEGG defined GSs. We observed a large number of significant GS-eQTL associations, in which the most significant associations arose between genetic variation and mRNA expression from the same GS. However, a number of associations involving genetic variation and mRNA expression from different GSs were also identified. Our proposed GS-eQTL method effectively addresses the multiple testing limitations in eQTL studies and provides biological context for SNP-expression associations.

Original languageEnglish (US)
Article numbere43301
JournalPLoS One
Volume7
Issue number8
DOIs
StatePublished - Aug 14 2012

Fingerprint

Gene expression
Genes
Gene Expression
gene expression
Messenger RNA
genetic variation
Single Nucleotide Polymorphism
genes
Quantitative Trait Loci
Gene Expression Regulation
Principal Component Analysis
testing
Testing
Genome
linkage (genetics)
Principal component analysis
quantitative trait loci
principal component analysis
statistical analysis
Statistical methods

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Identifying the genetic variation of gene expression using gene sets : Application of novel gene set eQTL approach to pharmGKB and KEGG. / Abo, Ryan; Jenkins, Gregory D.; Wang, Liewei M; Fridley, Brooke L.

In: PLoS One, Vol. 7, No. 8, e43301, 14.08.2012.

Research output: Contribution to journalArticle

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