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Prediction of gene functions is a major challenge to biologists in the post-genomic era. Interactions between genes and their products compose networks and can be used to infer gene functions. Most previous studies used heuristic approaches based on either local or global information of gene interaction networks to assign unknown gene functions. In this study, we propose a graph kernel-based method that can capture the structure of gene interaction networks to predict gene functions. We conducted an experimental study on a test-bed of P53-related genes. The experimental results demonstrated better performance for our proposed method as compared with baseline methods.