PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool
Summary: 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...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222003224 |
| _version_ | 1818639966111006720 |
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| author | Yen-Wei Chen Graciel Diamante Jessica Ding Thien Xuan Nghiem Jessica Yang Sung-Min Ha Peter Cohn Douglas Arneson Montgomery Blencowe Jennifer Garcia Nima Zaghari Paul Patel Xia Yang |
| author_facet | Yen-Wei Chen Graciel Diamante Jessica Ding Thien Xuan Nghiem Jessica Yang Sung-Min Ha Peter Cohn Douglas Arneson Montgomery Blencowe Jennifer Garcia Nima Zaghari Paul Patel Xia Yang |
| author_sort | Yen-Wei Chen |
| collection | DOAJ |
| description | Summary: 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 using in silico performance assessment. We further validated predicted drugs for nonalcoholic fatty liver disease in mice. By combining tissue- and species-specific in vivo drug signatures with gene networks, PharmOmics serves as a complementary tool to support drug characterization and network-based medicine. |
| first_indexed | 2024-12-16T23:03:46Z |
| format | Article |
| id | doaj.art-02dddb0194d8443180ce4ac7eada51d0 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-16T23:03:46Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-02dddb0194d8443180ce4ac7eada51d02022-12-21T22:12:37ZengElsevieriScience2589-00422022-04-01254104052PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning toolYen-Wei Chen0Graciel Diamante1Jessica Ding2Thien Xuan Nghiem3Jessica Yang4Sung-Min Ha5Peter Cohn6Douglas Arneson7Montgomery Blencowe8Jennifer Garcia9Nima Zaghari10Paul Patel11Xia Yang12Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular Toxicology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular Toxicology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular, Cellular, & Integrative Physiology, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular, Cellular, & Integrative Physiology, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USADepartment of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular Toxicology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular, Cellular, & Integrative Physiology, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program of Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Corresponding authorSummary: 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 using in silico performance assessment. We further validated predicted drugs for nonalcoholic fatty liver disease in mice. By combining tissue- and species-specific in vivo drug signatures with gene networks, PharmOmics serves as a complementary tool to support drug characterization and network-based medicine.http://www.sciencedirect.com/science/article/pii/S2589004222003224BioinformaticsBiocomputational methodSystems biologyIn silico biology |
| spellingShingle | Yen-Wei Chen Graciel Diamante Jessica Ding Thien Xuan Nghiem Jessica Yang Sung-Min Ha Peter Cohn Douglas Arneson Montgomery Blencowe Jennifer Garcia Nima Zaghari Paul Patel Xia Yang PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool iScience Bioinformatics Biocomputational method Systems biology In silico biology |
| title | PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool |
| title_full | PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool |
| title_fullStr | PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool |
| title_full_unstemmed | PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool |
| title_short | PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool |
| title_sort | pharmomics a species and tissue specific drug signature database and gene network based drug repositioning tool |
| topic | Bioinformatics Biocomputational method Systems biology In silico biology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222003224 |
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