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Issue 9, 2011
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Global risk transformative prioritization for prostate cancer candidate genes in molecular networks

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Abstract

Understanding the pathogenesis of complex diseases is aided by precise identification of the genes responsible. Many computational methods have been developed to prioritize candidate disease genes, but coverage of functional annotations may be a limiting factor for most of these methods. Here, we introduce a global candidate gene prioritization approach that considers information about network properties in the human protein interaction network and risk transformative contents from known disease genes. Global risk transformative scores were then used to prioritize candidate genes. This method was introduced to prioritize candidate genes for prostate cancer. The effectiveness of our global risk transformative algorithm for prioritizing candidate genes was evaluated according to validation studies. Compared with ToppGene and random walk-based methods, our method outperformed the two other candidate gene prioritization methods. The generality of our method was assessed by testing it on prostate cancer and other types of cancer. The performance was evaluated using standard leave-one-out cross-validation.

Graphical abstract: Global risk transformative prioritization for prostate cancer candidate genes in molecular networks

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Publication details

The article was received on 06 Apr 2011, accepted on 16 Jun 2011 and first published on 07 Jul 2011


Article type: Method
DOI: 10.1039/C1MB05134B
Citation: Mol. BioSyst., 2011,7, 2547-2553
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    Global risk transformative prioritization for prostate cancer candidate genes in molecular networks

    L. Chen, J. Tai, L. Zhang, Y. Shang, X. Li, X. Qu, W. Li, Z. Miao, X. Jia, H. Wang, W. Li and W. He, Mol. BioSyst., 2011, 7, 2547
    DOI: 10.1039/C1MB05134B

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