دورية أكاديمية
Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
| العنوان: | Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms. |
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| المؤلفون: | Wyatt B; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Davis AP; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Wiegers TC; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Wiegers J; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Abrar S; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Sciaky D; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Barkalow F; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Strong M; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States., Mattingly CJ; Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States. |
| المصدر: | Frontiers in toxicology [Front Toxicol] 2024 Jul 22; Vol. 6, pp. 1437884. Date of Electronic Publication: 2024 Jul 22 (Print Publication: 2024). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101777990 Publication Model: eCollection Cited Medium: Internet ISSN: 2673-3080 (Electronic) Linking ISSN: 26733080 NLM ISO Abbreviation: Front Toxicol Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne, Switzerland : Frontiers Research Foundation, [2019]- |
| مستخلص: | In environmental health, the specific molecular mechanisms connecting a chemical exposure to an adverse endpoint are often unknown, reflecting knowledge gaps. At the public Comparative Toxicogenomics Database (CTD; https://ctdbase.org/), we integrate manually curated, literature-based interactions from CTD to compute four-unit blocks of information organized as a potential step-wise molecular mechanism, known as "CGPD-tetramers," wherein a chemical interacts with a gene product to trigger a phenotype which can be linked to a disease. These computationally derived datasets can be used to fill the gaps and offer testable mechanistic information. Users can generate CGPD-tetramers for any combination of chemical, gene, phenotype, and/or disease of interest at CTD; however, such queries typically result in the generation of thousands of CGPD-tetramers. Here, we describe a novel approach to transform these large datasets into user-friendly chord diagrams using R. This visualization process is straightforward, simple to implement, and accessible to inexperienced users that have never used R before. Combining CGPD-tetramers into a single chord diagram helps identify potential key chemicals, genes, phenotypes, and diseases. This visualization allows users to more readily analyze computational datasets that can fill the exposure knowledge gaps in the environmental health continuum. Competing Interests: The 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 © 2024 Wyatt, Davis, Wiegers, Wiegers, Abrar, Sciaky, Barkalow, Strong and Mattingly.) |
| References: | Database (Oxford). 2011 Sep 20;2011:bar034. (PMID: 21933848) Toxicol Sci. 2020 Oct 1;177(2):392-404. (PMID: 32663284) Curr Opin Toxicol. 2018 Jun 01;9:1-7. (PMID: 29682628) Environ Sci Technol. 2018 Jan 16;52(2):839-849. (PMID: 29236470) Chem Res Toxicol. 2023 Jun 19;36(6):838-847. (PMID: 37093963) Bioinformatics. 2014 Oct;30(19):2811-2. (PMID: 24930139) Int J Environ Res Public Health. 2023 Jan 28;20(3):. (PMID: 36767684) Environ Health Perspect. 2016 Aug;124(8):1136-40. (PMID: 26871594) Nucleic Acids Res. 2023 Jan 6;51(D1):D1257-D1262. (PMID: 36169237) BMC Med Genomics. 2008 Oct 09;1:48. (PMID: 18845002) Food Chem Toxicol. 2023 Jun;176:113781. (PMID: 37059384) Environ Sci Technol. 2016 May 3;50(9):4579-86. (PMID: 26759916) Microbiol Resour Announc. 2022 Nov 17;11(11):e0079522. (PMID: 36314910) Toxicol Sci. 2023 Sep 28;195(2):155-168. (PMID: 37486259) Toxicol Appl Pharmacol. 2021 Jan 15;411:115370. (PMID: 33338516) Environ Health Perspect. 2020 Dec;128(12):125002. (PMID: 33369481) Environ Health Perspect. 2016 Oct;124(10):1592-1599. (PMID: 27170236) Best Pract Res Clin Obstet Gynaecol. 2023 Feb;86:102298. (PMID: 36623980) J Affect Disord. 2023 Apr 14;327:315-329. (PMID: 36758875) Sci Total Environ. 2024 Jul 15;934:173420. (PMID: 38777049) |
| فهرسة مساهمة: | Keywords: chord diagram; data visualization; database; environmental health; molecular mechanisms; r; tetramers |
| تواريخ الأحداث: | Date Created: 20240806 Latest Revision: 20240807 |
| رمز التحديث: | 20240807 |
| مُعرف محوري في PubMed: | PMC11298510 |
| DOI: | 10.3389/ftox.2024.1437884 |
| PMID: | 39104826 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2673-3080 |
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| DOI: | 10.3389/ftox.2024.1437884 |