Finding disease specific alterations in the co-expression of genes

Motivation: Standard analysis routines for microarray data aim at differentially expressed genes. In this paper, we address the complementary problem of detecting sets of differentially co-expressed genes in two phenotypically distinct sets of expression profiles. Results: We introduce a score for differential co-expression and suggest a computationally efficient algorithm for finding high scoring sets of genes. The use of our novel method is demonstrated in the context of simulations and on real expression data from a clinical study.