biostudies-literatureChen YWUniversity of California Los AngelesNIDDK NIH HHSNational Institutes of HealthJDRF104052https://www.ebi.ac.uk/biostudies/studies/S-EPMC8957031biostudies-literatureUnknown25(4)Drug development has been hampered by a high failure rate in clinical trials due to our incomplete understanding of drug functions across organs and species. Therefore, elucidating species- and tissue-specific drug functions can provide insights into therapeutic efficacy, potential adverse effects, and interspecies differences necessary for effective translational medicine. Here, we present PharmOmics, a drug knowledgebase and analytical tool that is hosted on an interactive web server. Using tissue- and species-specific transcriptome data from human, mouse, and rat curated from different databases, we implemented a gene-network-based approach for drug repositioning. We demonstrate the potential of PharmOmics to retrieve known therapeutic drugs and identify drugs with tissue toxicity usingiSciencePharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool.PMC8957031R01 DK117850R01 DK104363Diamante GYang JHa SMCohn PChen YWNghiem TXDing JBlencowe MPatel PYang XGarcia JZaghari NArneson DfalsePharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool.Drug development has been hampered by a high failure rate in clinical trials due to our incomplete understanding of drug functions across organs and species. Therefore, elucidating species- and tissue-specific drug functions can provide insights into therapeutic efficacy, potential adverse effects, and interspecies differences necessary for effective translational medicine. Here, we present PharmOmics, a drug knowledgebase and analytical tool that is hosted on an interactive web server. Using tissue- and species-specific transcriptome data from human, mouse, and rat curated from different databases, we implemented a gene-network-based approach for drug repositioning. We demonstrate the potential of PharmOmics to retrieve known therapeutic drugs and identify drugs with tissue toxicity using2022-01-01T00:00:00Z2022 Apr2025-04-04T12:56:35.028Z2025-04-04T12:56:35.028ZS-EPMC89570313534545510.1016/j.isci.2022.104052