HWVoteRank: A Network-Based Voting Approach for Identifying Coding and Non-Coding Cancer Drivers

Abstract

Cancer drivers play an important role in regulating cell growth, cell cycles, and DNA replication. Identifying these cancer drivers provides cancer researchers with indispensable knowledge that has important implications for clinical decision making. Some methods have been recently proposed to identify coding and non-coding cancer drivers through controllability analysis in network and eigenvector centrality based on community detection. However, the performance of these methods is not satisfactory. In this work, we focus on the strategy of selecting a set of critical nodes in cancer-special network as cancer drivers, and propose a novel approach for identifying coding and non-coding drives via a network-based voting mechanism. We name our approach HWVoteRank. Compared with two recent methods to identify cancer drivers, CBNA and NIBNA, and three algorithms for identifying key nodes on BRCA dataset, our method can achieve the best efficiency. By analyzing the results, it is found that our approach has better ability in identifying miRNA cancer drivers. We also applied our approach to identification of drivers of miRNA during Epithelial–Mesenchymal transition and drivers for cancer subtype. Through literature research, we found that those drivers explored by our approach are of biological significance.

Keywords

• undirected weighted network
• cancer driver
• gene with/without mutation
• miRNA
• voting mechanism