ArticleBMC bioinformatics2008
Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression.Science (New York, N.Y.) · 2014Article
- The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Review
- Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study.Frontiers in cell and developmental biology · 2014Article
- Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach.Genome biology · 2014Article
- Geographical, environmental and pathophysiological influences on the human blood transcriptome.Current genetic medicine reports · 2013Article
- Genetic and nongenetic variation revealed for the principal components of human gene expression.Genetics · 2013Article
- Blood-informative transcripts define nine common axes of peripheral blood gene expression.PLoS genetics · 2013Article
- Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.Nature protocols · 2012Article
- Use of pleiotropy to model genetic interactions in a population.PLoS genetics · 2012Article
- Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans.PLoS genetics · 2011Article
- Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.PLoS genetics · 2011Article
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3 authors.
Funding
Abstract
backgroundThe combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by analyzing gene expression traits one at a time. As thousands of expression traits are typically analyzed, this can reduce power because of the need to correct for the number of hypothesis tests performed. In addition, gene expression traits exhibit a complex correlation structure, which is ignored when analyzing traits individually.
resultsTo address these issues, we applied two different multivariate dimension reduction techniques, the Singular Value Decomposition (SVD) and Independent Component Analysis (ICA) to gene expression traits derived from a cross between two strains of Saccharomyces cerevisiae. Both methods decompose the data into a set of meta-traits, which are linear combinations of all the expression traits. The meta-traits were enriched for several Gene Ontology categories including metabolic pathways, stress response, RNA processing, ion transport, retro-transposition and telomeric maintenance. Genome-wide linkage analysis was performed on the top 20 meta-traits from both techniques. In total, 21 eQTL were found, of which 11 are novel. Interestingly, both cis and trans-linkages to the meta-traits were observed.
conclusionThese results demonstrate that dimension reduction methods are a useful and complementary approach for probing the genetic architecture of gene expression variation.
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