Pafway: Pairwise Associations Between Functional Annotations In Biological Networks And Pathways

Motivation: Large gene networks can be dense and difficult to interpret in a biologically meaningful way.Results: Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this package to reveal associations between functional annotations in an Arabidopsis thaliana gene network.