ZODDs: A Zebrafish Organ-Specific and Dose-Response Database for Environmental Chemical Mixtures

Introduction

Environmental contaminants typically exist as complex mixtures, yet their combined effects and dose-response relationships remain poorly characterized. To address this gap, we constructed ZODDs, a Zebrafish Organ-Specific and Omics Dose-Response Database that integrates chemical, anatomical, and dose-response information with high-throughput omics data.

Methods

The database is organized into two components. The first component comprises a curated list of chemicals sourced from the STITCH database, which has been integrated with zebrafish gene expression datasets obtained from the Gene Expression Omnibus (GEO). The second component comprises a comprehensive collection of gene expression datasets specifically related to the anatomical systems of zebrafish, sourced from the Expression Atlas. For each study, the exposure design, concentration range, duration, or developmental stage was harmonized and mapped to standardized identifiers. Differentially expressed genes were recalculated using an in-house R script.

Results

The current version of ZODDs comprises over 300 zebrafish exposure experiments and 14 organ-specific transcriptomic datasets, organized into structured tables containing differentially expressed genes and associated metadata.

Conclusions

This resource enables integration with the ZFinfer-Mixture inference system for the exploration of organ-specific chemical exposure inferences, mixture interactions, and dose-response trends under environmentally relevant chemical exposure scenarios. In this study, we present a representative PFNA case study demonstrating how dose-related transcriptomic data can be applied within the zebrafish inference model. The case study illustrates how ZODDs can support dose-dependent interpretation of chemical-induced biological responses. Collectively, this zebrafish-centered mixture and omics platform provides a reusable data foundation to enhance our understanding of how environmental chemical mixtures affect different organs and potentially support the development of new approaches for regulatory chemical risk assessment.