Workflow of the DP_LCC method. i) The phenome-interactome network is constructed by integrating the PPI network, disease-gene associations and currently known phenotype similarity data. ii) Diffusion profiles of diseases and genes are calculated by a random walk over the PPI network with restart where similarities between phenotypes are incorporated. iii) Candidate genes are then prioritized according to their similarities with the disease diffusion profile. The numbers on the edges of phenome network indicate their pairwise similarities.