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

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 typical

SUBMITTER: Wyatt B 

PROVIDER: S-EPMC11298510 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature