title: ksRepo: a generalized platform for computational drug repositioning.
abstract: BACKGROUND
  Repositioning approved drug and small molecules in novel therapeutic areas is of key interest to the pharmaceutical industry. A number of promising computational techniques have been developed to aid in repositioning, however, the majority of available methodologies require highly specific data inputs that preclude the use of many datasets and databases. There is a clear unmet need for a generalized methodology that enables the integration of multiple types of both gene expression data and database schema.
  
  
  RESULTS
  ksRepo eliminates the need for a single microarray platform as input and allows for the use of a variety of drug and chemical exposure databases. We tested ksRepo's performance on a set of five prostate cancer datasets using the Comparative Toxicogenomics Database (CTD) as our database of gene-compound interactions. ksRepo successfully predicted significance for five frontline prostate cancer therapies, representing a significant enrichment from over 7000 CTD compounds, and achieved specificity similar to other repositioning methods.
  
  
  CONCLUSIONS
  We present ksRepo, which enables investigators to use any data inputs for computational drug repositioning. ksRepo is implemented in a series of four functions in the R statistical environment under a BSD3 license. Source code is freely available at http://github.com/adam-sam-brown/ksRepo. A vignette is provided to aid users in performing ksRepo analysis.
authors: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA. adambrown@fas.harvard.edu.
authors: Adam S
authors: AS
authors: Brown
authors: Boston Children's Hospital, Boston, MA, 02115, USA. sekwon.kong@childrens.harvard.edu.
authors: Sek Won
authors: SW
authors: Kong
authors: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA. isaac_kohane@harvard.edu.
authors: Isaac S
authors: IS
authors: Kohane
authors: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA. Chirag_Patel@hms.harvard.edu.
authors: Chirag J
authors: CJ
authors: Patel
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D058492:Drug Repositioning / Q000379:methods*; D006801:Humans; D008297:Male; D008962:Models, Theoretical; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D011471:Prostatic Neoplasms / Q000188:drug therapy / Q000235:genetics*; D012984:Software; D043922:Toxicogenetics / Q000379:methods*
chemical_list: D004364:Pharmaceutical Preparations