An empirical Bayes approach for multiple tissue eQTL analysis. 2018

Gen Li, and Andrey A Shabalin, and Ivan Rusyn, and Fred A Wright, and Andrew B Nobel
Department of Biostatistics, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY, 10032 USA gl2521@cumc.columbia.edu.

Expression quantitative trait locus (eQTL) analyses identify genetic markers associated with the expression of a gene. Most up-to-date eQTL studies consider the connection between genetic variation and expression in a single tissue. Multi-tissue analyses have the potential to improve findings in a single tissue, and elucidate the genotypic basis of differences between tissues. In this article, we develop a hierarchical Bayesian model (MT-eQTL) for multi-tissue eQTL analysis. MT-eQTL explicitly captures patterns of variation in the presence or absence of eQTL, as well as the heterogeneity of effect sizes across tissues. We devise an efficient Expectation-Maximization (EM) algorithm for model fitting. Inferences concerning eQTL detection and the configuration of eQTL across tissues are derived from the adaptive thresholding of local false discovery rates, and maximum a posteriori estimation, respectively. We also provide theoretical justification of the adaptive procedure. We investigate the MT-eQTL model through an extensive analysis of a 9-tissue data set from the GTEx initiative.

UI MeSH Term Description Entries
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001499 Bayes Theorem A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result. Bayesian Analysis,Bayesian Estimation,Bayesian Forecast,Bayesian Method,Bayesian Prediction,Analysis, Bayesian,Bayesian Approach,Approach, Bayesian,Approachs, Bayesian,Bayesian Approachs,Estimation, Bayesian,Forecast, Bayesian,Method, Bayesian,Prediction, Bayesian,Theorem, Bayes
D015233 Models, Statistical Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc. Probabilistic Models,Statistical Models,Two-Parameter Models,Model, Statistical,Models, Binomial,Models, Polynomial,Statistical Model,Binomial Model,Binomial Models,Model, Binomial,Model, Polynomial,Model, Probabilistic,Model, Two-Parameter,Models, Probabilistic,Models, Two-Parameter,Polynomial Model,Polynomial Models,Probabilistic Model,Two Parameter Models,Two-Parameter Model
D015870 Gene Expression The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION. Expression, Gene,Expressions, Gene,Gene Expressions
D056808 Biostatistics The application of STATISTICS to biological systems and organisms involving the retrieval or collection, analysis, reduction, and interpretation of qualitative and quantitative data. Biological Statistics,Biological Statistic,Statistic, Biological,Statistics, Biological
D060005 Genotyping Techniques Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms). Genotype Assignment Methodology,Genotype Calling Methods,Genotype Determination Methods,Assignment Methodologies, Genotype,Assignment Methodology, Genotype,Calling Method, Genotype,Calling Methods, Genotype,Determination Method, Genotype,Determination Methods, Genotype,Genotype Assignment Methodologies,Genotype Calling Method,Genotype Determination Method,Genotyping Technique,Method, Genotype Calling,Method, Genotype Determination,Methodologies, Genotype Assignment,Methodology, Genotype Assignment,Methods, Genotype Calling,Methods, Genotype Determination,Technique, Genotyping,Techniques, Genotyping
D023281 Genomics The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural
D040641 Quantitative Trait Loci Genetic loci associated with a quantitative trait. Quantitative Trait Loci Genes,Loci, Quantitative Trait,Locus, Quantitative Trait,Quantitative Trait Locus,Trait Loci, Quantitative,Trait Locus, Quantitative

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