Prioritizing disease genes by bi-random walk

Authors:
Maoqiang Xie;Taehyun Hwang;Rui Kuang
Affiliations:
College of Software, Nankai University, Tianjin, China;Masonic Cancer Center, University of Minnesota, Twin Cities;Department of Computer Science and Engineering, University of Minnesota, Twin Cities
Venue:
PAKDD'12 Proceedings of the 16th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part II
Year:
2012

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Abstract

Random walk methods have been successfully applied to prioritizing disease causal genes. In this paper, we propose a bi-random walk algorithm (BiRW) based on a regularization framework for graph matching to globally prioritize disease genes for all phenotypes simultaneously. While previous methods perform random walk either on the protein-protein interaction network or the complete phenome-genome heterogenous network, BiRW performs random walk on the Kronecker product graph between the protein-protein interaction network and the phenotype similarity network. Three variations of BiRW that perform balanced or unbalanced bi-directional random walks are analyzed and compared with other random walk methods. Experiments on analyzing the disease phenotype-gene associations in Online Mendelian Inheritance in Man (OMIM) demonstrate that BiRW effectively improved disease gene prioritization over existing methods by ranking more known associations in the top 100 out of nearly 10,000 candidate genes.