Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.

作者信息

Wyatt Brent, Davis Allan Peter, Wiegers Thomas C, Wiegers Jolene, Abrar Sakib, Sciaky Daniela, Barkalow Fern, Strong Melissa, Mattingly Carolyn J

机构信息

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.

出版信息

Front Toxicol. 2024 Jul 22;6:1437884. doi: 10.3389/ftox.2024.1437884. eCollection 2024.

Abstract

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.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/27b6/11298510/797aad1dfada/ftox-06-1437884-g001.jpg

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