title: Computational Study of Drugs by Integrating Omics Data with Kernel Methods.
abstract: With the rapid development of genomic and chemogenomic techniques, many omics data sources for drugs have been publicly available. These data sources illustrate drug's biological function in the living cell from different levels and different aspects. One straightforward idea is to learn understandable rules via computational models and algorithms to mine and integrate these data sources. Here, we review our recent efforts on developing kernel-based methods to integrate drug related omics data sources. Three promising applications of our framework are shown to predict drug targets, assign drug's ATC-code annotation, and reveal drug repositioning. We demonstrate that data integration does provide more information and improve the accuracy by recovering more experimentally observed target proteins, ATC-codes, and drug repositioning. Importantly, data integration can indicate novel predictions which are supported by database search and functional annotation analysis and worthy of further experimental validation. In conclusion, kernel methods can efficiently integrate heterogeneous data sources to computationally study drugs, and will promote the further research in drug discovery in a low-cost way.
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23, Xinning Road, Xining, Qinghai Province, P. R. China.
authors.forename: Yongcui C
authors.initials: YC
authors.lastname: Wang
authors.affiliation: College of Science, China Agriculture University, No. 17. Qinghua East Road, Beijing, P. R. China.
authors.forename: Naiyang
authors.initials: N
authors.lastname: Deng
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23, Xinning Road, Xining, Qinghai Province, P. R. China. slchen@nwipb.cas.cn.
authors.forename: Shilong
authors.initials: S
authors.lastname: Chen
authors.affiliation: National Centre for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, N0.55, Zhongguancun East Road, Beijing, P. R. China. ywang@amss.ac.cn.|Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. ywang@amss.ac.cn.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
keywords: ATC-codes of drugs; Data integration; Drug repositioning; Drug-targets; Kernel methods; Omics data