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Enhanced QSAR Model Performance by Integrating Structural and Gene Expression Information
Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
* Author to whom correspondence should be addressed.
Received: 14 June 2013; in revised form: 20 July 2013 / Accepted: 26 July 2013 / Published: 4 September 2013
Abstract: Despite decades of intensive research and a number of demonstrable successes, quantitative structure-activity relationship (QSAR) models still fail to yield predictions with reasonable accuracy in some circumstances, especially when the QSAR paradox occurs. In this study, to avoid the QSAR paradox, we proposed a novel integrated approach to improve the model performance through using both structural and biological information from compounds. As a proof-of-concept, the integrated models were built on a toxicological dataset to predict non-genotoxic carcinogenicity of compounds, using not only the conventional molecular descriptors but also expression profiles of significant genes selected from microarray data. For test set data, our results demonstrated that the prediction accuracy of QSAR model was dramatically increased from 0.57 to 0.67 with incorporation of expression data of just one selected signature gene. Our successful integration of biological information into classic QSAR model provided a new insight and methodology for building predictive models especially when QSAR paradox occurred.
Keywords: quantitative structure-activity relationships (QSAR); SAR paradox; molecular modeling; gene expression; integrative analysis
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MDPI and ACS Style
Chen, Q.; Wu, L.; Liu, W.; Xing, L.; Fan, X. Enhanced QSAR Model Performance by Integrating Structural and Gene Expression Information. Molecules 2013, 18, 10789-10801.
Chen Q, Wu L, Liu W, Xing L, Fan X. Enhanced QSAR Model Performance by Integrating Structural and Gene Expression Information. Molecules. 2013; 18(9):10789-10801.
Chen, Qian; Wu, Leihong; Liu, Wei; Xing, Li; Fan, Xiaohui. 2013. "Enhanced QSAR Model Performance by Integrating Structural and Gene Expression Information." Molecules 18, no. 9: 10789-10801.