MOTIVATION: We consider the problem of multiple locus linkage analysis for expression traits of genes in a pathway or a network. To capitalize on co-expression of functionally related genes, we propose a penalized regression method that maps multiple expression quantitative trait loci (eQTLs) for all related genes simultaneously while accounting for their shared functions as specified a priori by a gene pathway or network. RESULTS: An analysis of a mouse dataset and simulation studies clearly demonstrate the advantage of the proposed method over a standard approach that ignores biological knowledge of gene networks.
