Prediction of survival risks with adjusted gene expression through risk-gene networks
- Authors
- Lee, Minhyeok; Han, Sung Won; Seok, Junhee
- Issue Date
- Dec-2019
- Publisher
- OXFORD UNIV PRESS
- Citation
- BIOINFORMATICS, v.35, no.23, pp 4898 - 4906
- Pages
- 9
- Journal Title
- BIOINFORMATICS
- Volume
- 35
- Number
- 23
- Start Page
- 4898
- End Page
- 4906
- URI
- https://scholarworks.bwise.kr/cau/handle/2019.sw.cau/75247
- DOI
- 10.1093/bioinformatics/btz399
- ISSN
- 1367-4803
1367-4811
- Abstract
- Motivation: Network-based analysis of biomedical data has been extensively studied over the last decades. As a successful application, gene networks have been used to illustrate interactions among genes and explain the associated phenotypes. However, the gene network approaches have not been actively applied for survival analysis, which is one of the main interests of biomedical research. In addition, a few previous studies using gene networks for survival analysis construct networks mainly from prior knowledge, such as pathways, regulations and gene sets, while the performance considerably depends on the selection of prior knowledge. Results: In this paper, we propose a data-driven construction method for survival risk-gene networks as well as a survival risk prediction method using the network structure. The proposed method constructs risk-gene networks with survival-associated genes using penalized regression. Then, gene expression indices are hierarchically adjusted through the networks to reduce the variance intrinsic in datasets. By illustrating risk-gene structure, the proposed method is expected to provide an intuition for the relationship between genes and survival risks. The risk-gene network is applied to a low grade glioma dataset, and produces a hypothesis of the relationship between genetic biomarkers of low and high grade glioma. Moreover, with multiple datasets, we demonstrate that the proposed method shows superior prediction performance compared to other conventional methods.
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Collections - College of ICT Engineering > School of Electrical and Electronics Engineering > 1. Journal Articles
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