Comprehensive evaluation of computational methods for predicting cancer driver genes

Optimal methods could effectively improve the accuracy of predicting and identifying candidate driver genes. Various computational methods based on mutational frequency, network and function approaches have been developed to identify mutation driver genes in cancer genomes. However, a comprehensive evaluation of the performance levels of network-, function- and frequency-based methods is lacking. In the present study, we assessed and compared eight performance criteria for eight network-based, one function-based and three frequency-based algorithms using eight benchmark datasets. Under different conditions, the performance of approaches varied in terms of network, measurement and sample size. The frequency-based driverMAPS and network-based HotNet2 methods showed the best overall performance. Network-based algorithms using protein–protein interaction networks outperformed the function- and the frequency-based approaches. Precision, F1 score and Matthews correlation coefficient were low for most approaches. Thus, most of these algorithms require stringent cutoffs to correctly distinguish driver and non-driver genes. We constructed a website named Cancer Driver Catalog (http://159.226.67.237/sun/cancer_driver/), wherein we integrated the gene scores predicted by the foregoing software programs. This resource provides valuable guidance for cancer researchers and clinical oncologists prioritizing cancer driver gene candidates by using an optimal tool.