title: A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS.
abstract: It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to select genes or pathways strongly associated with a clinical/biological outcome. Alternatively, in this paper, we propose a nonparametric Bayesian model for gene selection incorporating network information. In addition to identifying genes that have a strong association with a clinical outcome, our model can select genes with particular expressional behavior, in which case the regression models are not directly applicable. We show that our proposed model is equivalent to an infinity mixture model for which we develop a posterior computation algorithm based on Markov chain Monte Carlo (MCMC) methods. We also propose two fast computing algorithms that approximate the posterior simulation with good accuracy but relatively low computational cost. We illustrate our methods on simulation studies and the analysis of Spellman yeast cell cycle microarray data.
authors.affiliation: Department of Biostatistics and Bioinformatics Emory University 1518 Clifton Rd. Atlanta, Georgia 30322 USA.
authors.forename: Yize
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Biostatistics and Bioinformatics Emory University 1518 Clifton Rd. Atlanta, Georgia 30322 USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Kang
authors.affiliation: Department of Biostatistics and Bioinformatics Emory University 1518 Clifton Rd. Atlanta, Georgia 30322 USA.
authors.forename: Tianwei
authors.initials: T
authors.lastname: Yu
keywords: Dirichlet process mixture; density estimation; feature selection; ising priors; microarray data