Discovery Park

Bioinformatics Seminar

February 26 @ 4:30 PM - 5:30 PM - ME 1130

Date:  Tuesday, February 26, 2013
Time:  4:30 PM
Place: ME 1130

Speaker: Anindya Bhadra; Department of Statistics, Purdue University

Title: "Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis"

Abstract
We describe a Bayesian technique to (a) perform a sparse joint selection of significant predictor variables and significant inverse covariance matrix elements of the response variables in a high-dimensional linear Gaussian sparse seemingly unrelated regression (SSUR) setting and (b) perform an association analysis between the high- dimensional sets of predictors and responses in such a setting. To search the high-dimensional model space, where both the number of predictors and the number of possibly correlated responses can be larger than the sample size, we demonstrate that a marginalization-based collapsed Gibbs sampler, in combination with spike and slab type of priors, offers a computationally feasible and efficient solution. As an example, we apply our method to an expression quantitative trait loci (eQTL) analysis on publicly available single nucleotide polymorphism (SNP) and gene expression data for humans where the primary interest lies in finding the significant ass!
 ociations between the sets of SNPs and possibly correlated genetic transcripts. Our method also allows for inference on the sparse interaction network of the transcripts (response variables) after accounting for the effect of the SNPs (predictor variables). We exploit properties of Gaussian graphical models to make statements concerning conditional independence of the responses. Our method compares favorably to existing Bayesian approaches developed for this purpose.

Associated Reading:
Bhadra, A. and Mallick, B. K. (2013). Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis. (to appear, Biometrics) http://www.stat.purdue.edu/~doerge/BIOINFORM.D/SPRING13/Biometrics_Bhadra_Mallick.pdf
 

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