Bayesian meta-analysis for identifying periodically expressed genes in fission yeast cell cycle

Xiaodan Fan, Saumyadipta Pyne, Jun S. Liu

The Annals of Applied Statistics · 2010 · Volume 4 · Issue 2

Abstract

The effort to identify genes with periodic expression during the cell cycle from genome-wide microarray time series data has been ongoing for a decade. However, the lack of rigorous modeling of periodic expression as well as the lack of a comprehensive model for integrating information across genes and experiments has impaired the effort for the accurate identification of periodically expressed genes. To address the problem, we introduce a Bayesian model to integrate multiple independent microarray data sets from three recent genome-wide cell cycle studies on fission yeast. A hierarchical model was used for data integration. In order to facilitate an efficient Monte Carlo sampling from the joint posterior distribution, we develop a novel Metropolis–Hastings group move. A surprising finding from our integrated analysis is that more than 40% of the genes in fission yeast are significantly periodically expressed, greatly enhancing the reported 10–15% of the genes in the current literature. It calls for a reconsideration of the periodically expressed gene detection problem.

Keywords

cell cycle, fission yeast, Markov chain Monte Carlo, Meta-analysis, microarray time series, periodically expressed gene, Schizosaccharomyces pombe

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