From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures

Abstract

Abstract Motivation A critical element of drug development is the identification of therapeutic targets for diseases. However, the depletion of therapeutic targets is a serious problem. Results In this study, we propose the novel concept of target repositioning, an extension of the concept of drug repositioning, to predict new therapeutic targets for various diseases. Predictions were performed by a trans-disease analysis which integrated genetically perturbed transcriptomic signatures (knockdown of 4345 genes and overexpression of 3114 genes) and disease-specific gene transcriptomic signatures of 79 diseases. The trans-disease method, which takes into account similarities among diseases, enabled us to distinguish the inhibitory from activatory targets and to predict the therapeutic targetability of not only proteins with known target–disease associations but also orphan proteins without known associations. Our proposed method is expected to be useful for understanding the commonality of mechanisms among diseases and for therapeutic target identification in drug discovery. Availability and implementation Supplemental information and software are available at the following website [http://labo.bio.kyutech.ac.jp/~yamani/target_repositioning/]. Supplementary information Supplementary data are available at Bioinformatics online.