Extracting active pathways from gene expression data

MOTIVATION: A promising way to make sense out of gene expression profiles is to relate them to the activity of metabolic and signalling pathways. Each pathway usually involves many genes, such as enzymes, which can themselves participate in many pathways. The set of all known pathways can therefore be represented by a complex network of genes. Searching for regularities in the set of gene expression profiles with respect to the topology of this gene network is a way to automatically extract active pathways and their associated patterns of activity. METHOD: We present a method to perform this task, which consists in encoding both the gene network and the set of profiles into two kernel functions, and performing a regularized form of canonical correlation analysis between the two kernels. RESULTS: When applied to publicly available expression data the method is able to extract biologically relevant expression patterns, as well as pathways with related activity.