A Bayesian Approach for Graph-constrained Estimation for High-dimensional Regression.

Abstract

Many different biological processes are represented by network graphs such as regulatory networks, metabolic pathways, and protein-protein interaction networks. Since genes that are linked on the networks usually have biologically similar functions, the linked genes form molecular modules to affect the clinical phenotypes/outcomes. Similarly, in large-scale genetic association studies, many SNPs are in high linkage disequilibrium (LD), which can also be summarized as a LD graph. In order to incorporate the graph information into regression analysis with high dimensional genomic data as predictors, we introduce a Bayesian approach for graph-constrained estimation (Bayesian GRACE) and regularization, which controls the amount of regularization for sparsity and smoothness of the regression coefficients. The Bayesian estimation with their posterior distributions can provide credible intervals for the estimates of the regression coefficients along with standard errors. The deviance information criterion (DIC) is applied for model assessment and tuning parameter selection. The performance of the proposed Bayesian approach is evaluated through simulation studies and is compared with Bayesian Lasso and Bayesian Elastic-net procedures. We demonstrate our method in an analysis of data from a case-control genome-wide association study of neuroblastoma using a weighted LD graph.