An empirical Bayesian approach for identifying differential co-expression in high-throughput experiments. Biometrics E-publication before print: http://onlinelibrary.wiley.com/doi/10.1111/j.15410420.2011.01688.x/abstract

for Identifying Differential Co-expression in High-throughput Experiments A common goal of microarray and related high-throughput genomic experiments is to identify genes that vary across biological condition. Most often this is accomplished by identifying genes with changes in mean expression level, so called differentially expressed (DE) genes, and a number of effective methods for identifying DE genes have been developed. Although useful, these approaches do not accommodate other types of differential regulation. An important example concerns differential co-expression (DC). Investigations of this class of genes are hampered by the large cardinality of the space to be interrogated as well as by influential outliers. As a result, existing DC approaches are often underpowered, exceedingly prone to false discoveries, and/or computationally intractable for even a moderately large number of pairs. To address this, an empirical Bayesian approach for identifying DC gene pairs is developed. The approach provides a false discovery rate (FDR) controlled list of significant DC gene pairs without sacrificing power. It is applicable within a single study as well as across multiple studies. Computations are greatly facilitated by a modification to th