Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.22.163949v1?rss=1 Authors: Kim, S. Y., Choe, E. K., Shivakumar, M., Kim, D., Sohn, K.-A. Abstract: Motivation: To better understand the molecular features of cancers, a comprehensive analysis using multi-omics data has been conducted. Additionally, a pathway activity inference method has been developed to facilitate the integrative effects of multiple genes. In this respect, we have recently proposed a novel integrative pathway activity inference approach, iDRW, and demonstrated the effectiveness of the method with respect to dichotomizing two survival groups. However, there were several limitations, such as a lack of generality. In this study, we designed a directed gene-gene graph using pathway information by assigning interactions between genes in multiple layers of networks. Results: As a proof-of-concept study, it was evaluated using three genomic profiles of urologic cancer patients. The proposed integrative approach achieved improved outcome prediction performances compared with a single genomic profile alone and other existing pathway activity inference methods. The integrative approach also identified common/cancer-specific candidate driver pathways as predictive prognostic features in urologic cancers. Furthermore, it provides better biological insights into the prioritized pathways and genes in an integrated view using a multi-layered gene-gene network. Our framework is not specifically designed for urologic cancers and can be generally applicable for various datasets. Availability: iDRW is implemented as the R software package. The source codes are available at https://github.com/sykim122/iDRW. Copy rights belong to original authors. Visit the link for more info