دورية أكاديمية
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A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.

التفاصيل البيبلوغرافية
العنوان: A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.
المؤلفون: Douglass EF Jr; Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.; Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, GA 30602, USA., Allaway RJ; Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA., Szalai B; Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary., Wang W; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Tian T; Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China., Fernández-Torras A; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Realubit R; Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA., Karan C; Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA., Zheng S; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Pessia A; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Tanoli Z; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Jafari M; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Wan F; Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China., Li S; Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China., Xiong Y; Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China., Duran-Frigola M; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Bertoni M; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Badia-I-Mompel P; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Mateo L; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Guitart-Pla O; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain., Chung V; Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA., Tang J; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland., Zeng J; Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China., Aloy P; Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain., Saez-Rodriguez J; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany., Guinney J; Computational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA., Gerhard DS; Office of Cancer Genomics, National Cancer Institute, NIH, Bethesda, MD 20892, USA., Califano A; Department of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.; Department of Medicine, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, USA.; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, 701 W 168th Street, New York, NY 10032, USA.; Department of Biomedical Informatics, Columbia University Irving Medical Center, 622 W 168th Street, New York, NY 10032, USA.
مؤلفون مشاركون: DREAM CTD-squared Pancancer Drug Activity Challenge Consortium
المصدر: Cell reports. Medicine [Cell Rep Med] 2022 Jan 18; Vol. 3 (1), pp. 100492. Date of Electronic Publication: 2022 Jan 18 (Print Publication: 2022).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Cell Press Country of Publication: United States NLM ID: 101766894 Publication Model: eCollection Cited Medium: Internet ISSN: 2666-3791 (Electronic) Linking ISSN: 26663791 NLM ISO Abbreviation: Cell Rep Med Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [Cambridge, MA] : Cell Press, [2020]-
مواضيع طبية MeSH: Polypharmacology*, Neoplasms/*drug therapy, Algorithms ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Neural Networks, Computer ; Protein Kinases/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription, Genetic
مستخلص: The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with ∼400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among ∼1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action.
Competing Interests: A.C. is founder, equity holder, and consultant of DarwinHealth, Inc., a company that has licensed the PANACEA database used in this manuscript from Columbia University. Columbia University is also an equity holder in DarwinHealth, Inc. J.S.-R. has received funding from GSK and Sanofi and personal fees from Travere Therapeutics. B.S. received consultation fees from Turbine, Ltd. All other authors declare no competing interests.
(© 2021.)
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معلومات مُعتمدة: U01 CA217862 United States CA NCI NIH HHS; S10 OD021764 United States OD NIH HHS; S10 OD012351 United States OD NIH HHS; U01 CA168426 United States CA NCI NIH HHS; U01 CA217858 United States CA NCI NIH HHS
فهرسة مساهمة: Keywords: DREAM challenge; community challenge; pharmacogenomics; polypharmacology
المشرفين على المادة: 0 (RNA, Messenger)
EC 2.7.- (Protein Kinases)
تواريخ الأحداث: Date Created: 20220202 Date Completed: 20220304 Latest Revision: 20221206
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC8784774
DOI: 10.1016/j.xcrm.2021.100492
PMID: 35106508
قاعدة البيانات: MEDLINE
الوصف
تدمد:2666-3791
DOI:10.1016/j.xcrm.2021.100492