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The study of disease-relevant gene modules is one of the main methods to discover disease pathway and potential drug targets. Recent studies have found that most disease proteins tend to form many separate connected components and scatter across the protein-protein interaction network. However, most of the research on discovering disease modules are biased toward well-studied seed genes, which tend to extend seed genes into a single connected subnetwork. In this paper, we propose N2V-HC, an algorithm framework aiming to unbiasedly discover the scattered disease modules based on deep representation learning of integrated multi-layer biological networks. Our method first predicts disease associated genes based on summary data of Genome-wide Association Studies (GWAS) and expression Quantitative Trait Loci (eQTL) studies, and generates an integrated network on the basis of human interactome. The features of nodes in the network are then extracted by deep representation learning. Hierarchical clustering with dynamic tree cut methods are applied to discover the modules that are enriched with disease associated genes. The evaluation on real networks and simulated networks show that N2V-HC performs better than existing methods in network module discovery. Case studies on Parkinson's disease and Alzheimer's disease, show that N2V-HC can be used to discover biological meaningful modules related to the pathways underlying complex diseases.

Disease Module Identification Based on Representation Learning of Complex Networks Integrated From GWAS, eQTL Summaries, and Human Interactome