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CPT Pharmacometrics Syst Pharmacol. 2016 Nov;5(11):599-607. doi: 10.1002/psp4.12108. Epub 2016 Nov 14.

Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses.

Paik H1,2, Chen B1,2, Sirota M1,2, Hadley D1,2, Butte AJ1,2.

Author information

1
Institute for Computational Health Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA.
2
Department of Pediatrics, School of Medicine, University of California - San Francisco, San Francisco, California, USA.

Abstract

Drug repositioning has been based largely on genomic signatures of drugs and diseases. One challenge in these efforts lies in connecting the molecular signatures of drugs into clinical responses, including therapeutic and side effects, to the repurpose of drugs. We addressed this challenge by evaluating drug-drug relationships using a phenotypic and molecular-based approach that integrates therapeutic indications, side effects, and gene expression profiles induced by each drug. Using cosine similarity, relationships between 445 drugs were evaluated based on high-dimensional spaces consisting of phenotypic terms of drugs and genomic signatures, respectively. One hundred fifty-one of 445 drugs comprising 450 drug pairs displayed significant similarities in both phenotypic and genomic signatures (P value < 0.05). We also found that similar gene expressions of drugs do indeed yield similar clinical phenotypes. We generated similarity matrixes of drugs using the expression profiles they induce in a cell line and phenotypic effects.

PMID:
27860440
PMCID:
PMC5192994
DOI:
10.1002/psp4.12108
[Indexed for MEDLINE]
Free PMC Article

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