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bioRxiv · 10.1101/2020.07.22.163949

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer

Kim, S. Y.·Choe, E. K.·Shivakumar, M.·Kim, D.·Sohn, K.-A.
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Abstract

MotivationTo 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. ResultsAs 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. AvailabilityiDRW is implemented as the R software package. The source codes are available at https://github.com/sykim122/iDRW.

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Kim, S. Y., Choe, E. K., Shivakumar, M., Kim, D., Sohn, K.-A.. 2020-07-24. Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. https://doi.org/10.1101/2020.07.22.163949

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