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An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations

Lookup NU author(s): Joseph Mullen, Dr Simon CockellORCiD, Professor Anil Wipat



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Drug development is both increasing in cost whilst decreasing in productivity. There is a general acceptance that the current paradigm of R&D needs to change. One alternative approach is drug repositioning. With target-based approaches utilised heavily in the field of drug discovery, it becomes increasingly necessary to have a systematic method to rank gene-disease associations. Although methods already exist to collect, integrate and score these associations, they are often not a reliable reflection of expert knowledge. Furthermore, the amount of data available in all areas covered by bioinformatics is increasing dramatically year on year. It thus makes sense to move away from more generalised hypothesis driven approaches to research to one that allows data to generate their own hypothesis. We introduce an integrated, data driven approach to drug repositioning. We first apply a Bayesian statistics approach to rank 309,885 gene-disease associations using existing knowledge. Ranked associations are then integrated with other biological data to produce a semantically-rich drug discovery network. Using this network, we show how our approach identifies diseases of the central nervous system (CNS) to be an area of interest. CNS disorders are identified due to the low numbers of such disorders that currently have marketed treatments, in comparison to other therapeutic areas. We then systematically mine our network for semantic subgraphs that allow us to infer drug-disease relations that are not captured in the network. We identify and rank 275,934 drug-disease has_indication associations after filtering those that are more likely to be side effects, whilst commenting on the top ranked associations in more detail. The dataset has been created in Neo4j and is available for download at along with a Java implementation of the searching algorithm.

Publication metadata

Author(s): Mullen J, Cockell SJ, Woollard P, Wipat A

Publication type: Article

Publication status: Published

Journal: PLoS One

Year: 2016

Volume: 11

Issue: 5

Online publication date: 19/05/2016

Acceptance date: 04/05/2016

Date deposited: 01/07/2016

ISSN (print): 1932-6203

Publisher: Public Library of Science


DOI: 10.1371/journal.pone.0155811


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Funder referenceFunder name
CASE scholarship from GlaxoSmithKline (GSK)
1592752Engineering and Physical Sciences Research Council (EPSRC)