A Bayesian Model for Biclustering with Applications

Abstract

Summary The paper proposes a Bayesian method for biclustering with applications to gene microarray studies, where we want to cluster genes and experimental conditions simultaneously. We begin by embedding bicluster analysis into the framework of a plaid model with random effects. The corresponding likelihood is then regularized by the hierarchical priors in each layer. The resulting posterior, which is asymptotically equivalent to a penalized likelihood, can attenuate the effect of high dimensionality on cluster predictions. We provide an empirical Bayes algorithm for sampling posteriors, in which we estimate the cluster memberships of all genes and samples by maximizing an explicit marginal posterior of these memberships. The new algorithm makes the estimation of the Bayesian plaid model computationally feasible and efficient. The performance of our procedure is evaluated on both simulated and real microarray gene expression data sets. The numerical results show that our proposal substantially outperforms the original plaid model in terms of misclassification rates across a range of scenarios. Applying our method to two yeast gene expression data sets, we identify several new biclusters which show the enrichment of known annotations of yeast genes.