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Predicting candidate genes based on combined network topological features: a case study in coronary artery disease.

ABSTRACT: Predicting candidate genes using gene expression profiles and unbiased protein-protein interactions (PPI) contributes a lot in deciphering the pathogenesis of complex diseases. Recent studies showed that there are significant disparities in network topological features between non-disease and disease genes in protein-protein interaction settings. Integrated methods could consider their characteristics comprehensively in a biological network. In this study, we introduce a novel computational method, based on combined network topological features, to construct a combined classifier and then use it to predict candidate genes for coronary artery diseases (CAD). As a result, 276 novel candidate genes were predicted and were found to share similar functions to known disease genes. The majority of the candidate genes were cross-validated by other three methods. Our method will be useful in the search for candidate genes of other diseases.

SUBMITTER: Zhang L

PROVIDER: S-EPMC3382204 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Predicting candidate genes based on combined network topological features: a case study in coronary artery disease.

Zhang Liangcai L Li Xu X Tai Jingxie J Li Wan W Chen Lina L

PloS one 20120622 6

Predicting candidate genes using gene expression profiles and unbiased protein-protein interactions (PPI) contributes a lot in deciphering the pathogenesis of complex diseases. Recent studies showed that there are significant disparities in network topological features between non-disease and disease genes in protein-protein interaction settings. Integrated methods could consider their characteristics comprehensively in a biological network. In this study, we introduce a novel computational meth ...[more]

PMID: 22761820

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