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BioMed Research International
Volume 2018, Article ID 4028473, 6 pages
https://doi.org/10.1155/2018/4028473
Research Article

The Prediction of Drug-Disease Correlation Based on Gene Expression Data

1School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
2Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
3Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
4College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai 201306, China
5IPQ Analytics, LLC/Strategic Medicine, Philadelphia, PA, USA
6Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 30007, China

Correspondence should be addressed to Ying Yu; nc.ca.sbis@gniyuy and Lu Xie; moc.kooltuo@7102xeixul

Received 11 November 2017; Revised 18 January 2018; Accepted 11 February 2018; Published 25 March 2018

Academic Editor: Jialiang Yang

Copyright © 2018 Hui Cui et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The explosive growth of high-throughput experimental methods and resulting data yields both opportunity and challenge for selecting the correct drug to treat both a specific patient and their individual disease. Ideally, it would be useful and efficient if computational approaches could be applied to help achieve optimal drug-patient-disease matching but current efforts have met with limited success. Current approaches have primarily utilized the measureable effect of a specific drug on target tissue or cell lines to identify the potential biological effect of such treatment. While these efforts have met with some level of success, there exists much opportunity for improvement. This specifically follows the observation that, for many diseases in light of actual patient response, there is increasing need for treatment with combinations of drugs rather than single drug therapies. Only a few previous studies have yielded computational approaches for predicting the synergy of drug combinations by analyzing high-throughput molecular datasets. However, these computational approaches focused on the characteristics of the drug itself, without fully accounting for disease factors. Here, we propose an algorithm to specifically predict synergistic effects of drug combinations on various diseases, by integrating the data characteristics of disease-related gene expression profiles with drug-treated gene expression profiles. We have demonstrated utility through its application to transcriptome data, including microarray and RNASeq data, and the drug-disease prediction results were validated using existing publications and drug databases. It is also applicable to other quantitative profiling data such as proteomics data. We also provide an interactive web interface to allow our Prediction of Drug-Disease method to be readily applied to user data. While our studies represent a preliminary exploration of this critical problem, we believe that the algorithm can provide the basis for further refinement towards addressing a large clinical need.