دورية أكاديمية
أعرض في EDS

Assessing network-based methods in the context of system toxicology.

التفاصيل البيبلوغرافية
العنوان: Assessing network-based methods in the context of system toxicology.
المؤلفون: Valls-Margarit J; Medbioinformatics Solutions SL, Barcelona, Spain., Piñero J; Medbioinformatics Solutions SL, Barcelona, Spain., Füzi B; Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria., Cerisier N; Université Paris Cité, CNRS, INSERM U1133, Unité de Biologie Fonctionnelle et Adaptative, Paris, France., Taboureau O; Université Paris Cité, CNRS, INSERM U1133, Unité de Biologie Fonctionnelle et Adaptative, Paris, France., Furlong LI; Medbioinformatics Solutions SL, Barcelona, Spain.
المصدر: Frontiers in pharmacology [Front Pharmacol] 2023 Jul 12; Vol. 14, pp. 1225697. Date of Electronic Publication: 2023 Jul 12 (Print Publication: 2023).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Frontiers Media] Country of Publication: Switzerland NLM ID: 101548923 Publication Model: eCollection Cited Medium: Print ISSN: 1663-9812 (Print) Linking ISSN: 16639812 NLM ISO Abbreviation: Front Pharmacol Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [Lausanne : Frontiers Media]
مستخلص: Introduction: Network-based methods are promising approaches in systems toxicology because they can be used to predict the effects of drugs and chemicals on health, to elucidate the mode of action of compounds, and to identify biomarkers of toxicity. Over the years, the network biology community has developed a wide range of methods, and users are faced with the task of choosing the most appropriate method for their own application. Furthermore, the advantages and limitations of each method are difficult to determine without a proper standard and comparative evaluation of their performance. This study aims to evaluate different network-based methods that can be used to gain biological insight into the mechanisms of drug toxicity, using valproic acid (VPA)-induced liver steatosis as a benchmark. Methods: We provide a comprehensive analysis of the results produced by each method and highlight the fact that the experimental design (how the method is applied) is relevant in addition to the method specifications. We also contribute with a systematic methodology to analyse the results of the methods individually and in a comparative manner. Results: Our results show that the evaluated tools differ in their performance against the benchmark and in their ability to provide novel insights into the mechanism of adverse effects of the drug. We also suggest that aggregation of the results provided by different methods provides a more confident set of candidate genes and processes to further the knowledge of the drug's mechanism of action. Discussion: By providing a detailed and systematic analysis of the results of different network-based tools, we aim to assist users in making informed decisions about the most appropriate method for systems toxicology applications.
Competing Interests: JV-M, LF, and JP are employees of Medbioinformatics Solutions SL. JP and LF are co-founders and hold shares of Medbioinformatics Solutions SL. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Valls-Margarit, Piñero, Füzi, Cerisier, Taboureau and Furlong.)
References: Nat Commun. 2021 Mar 19;12(1):1796. (PMID: 33741907)
Science. 2015 Jan 23;347(6220):1260419. (PMID: 25613900)
Nat Rev Genet. 2011 Jan;12(1):56-68. (PMID: 21164525)
Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198. (PMID: 31066453)
Bioinformatics. 2019 Dec 15;35(24):5391-5392. (PMID: 31329252)
Toxicol Appl Pharmacol. 2020 Oct 15;405:115210. (PMID: 32860831)
Front Endocrinol (Lausanne). 2019 Jun 26;10:411. (PMID: 31293521)
Nat Commun. 2018 Jun 29;9(1):2544. (PMID: 29959323)
Proteomics. 2013 Apr;13(7):1065-76. (PMID: 23386401)
Biomedicines. 2022 Jan 17;10(1):. (PMID: 35052872)
Clin Mol Hepatol. 2013 Sep;19(3):210-5. (PMID: 24133660)
J Cheminform. 2017 Aug 14;9(1):45. (PMID: 29086168)
Bioinformatics. 2005 Feb 1;21(3):364-78. (PMID: 15374873)
Bioinformatics. 2006 Jul 1;22(13):1600-7. (PMID: 16606683)
Nucleic Acids Res. 2015 Jul 1;43(W1):W612-20. (PMID: 25883136)
iScience. 2023 Jan 31;26(3):106094. (PMID: 36895646)
Nucleic Acids Res. 2023 Jan 6;51(D1):D1257-D1262. (PMID: 36169237)
PLoS One. 2011;6(7):e21800. (PMID: 21789182)
Nat Rev Drug Discov. 2023 Feb;22(2):145-162. (PMID: 36261593)
Nat Protoc. 2019 Feb;14(2):482-517. (PMID: 30664679)
Nucleic Acids Res. 2019 Jan 8;47(D1):D930-D940. (PMID: 30398643)
PLoS One. 2012;7(9):e43557. (PMID: 23028459)
J Mol Biol. 2019 Jun 14;431(13):2477-2484. (PMID: 30851278)
Brief Bioinform. 2022 Jul 18;23(4):. (PMID: 35704883)
Nat Methods. 2019 Sep;16(9):843-852. (PMID: 31471613)
Nucleic Acids Res. 2020 Jan 8;48(D1):D845-D855. (PMID: 31680165)
Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):882-7. (PMID: 21187432)
Nucleic Acids Res. 2017 Jan 4;45(D1):D932-D939. (PMID: 27789690)
Bioinformatics. 2014 Jun 15;30(12):i219-27. (PMID: 24931987)
Endocrinology. 2012 Feb;153(2):583-91. (PMID: 22147010)
J Cheminform. 2023 Jan 6;15(1):3. (PMID: 36609528)
Nat Rev Genet. 2017 Sep;18(9):551-562. (PMID: 28607512)
Bioinformatics. 2017 Sep 15;33(18):2938-2940. (PMID: 28645171)
Trends Pharmacol Sci. 2022 Feb;43(2):136-150. (PMID: 34895945)
Bioinformatics. 2020 Jun 1;36(12):3920-3921. (PMID: 32271874)
World J Hepatol. 2015 May 28;7(9):1251-7. (PMID: 26019740)
Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082. (PMID: 29126136)
معلومات مُعتمدة: W 1232 Austria FWF_ Austrian Science Fund FWF
فهرسة مساهمة: Keywords: drug adverse reactions; drug toxicity; interactome; multiscale network model; network biology; network propagation; systems toxicology
تواريخ الأحداث: Date Created: 20230728 Latest Revision: 20240214
رمز التحديث: 20240214
مُعرف محوري في PubMed: PMC10369070
DOI: 10.3389/fphar.2023.1225697
PMID: 37502213
قاعدة البيانات: MEDLINE
الوصف
تدمد:1663-9812
DOI:10.3389/fphar.2023.1225697