Leveraging ontologies to predict biological activity of chemicals across genes
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arXiv
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| Autores principales: | , , , , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866917118208901120 |
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| author | Kampe, Jennifer N. Dunson, David B. Carberry, Celeste K. Rager, Julia E. Zilber, Daniel Messier, Kyle P. |
| author_facet | Kampe, Jennifer N. Dunson, David B. Carberry, Celeste K. Rager, Julia E. Zilber, Daniel Messier, Kyle P. |
| contents | High-throughput screening (HTS) is useful for evaluating chemicals for potential human health risks. However, given the extraordinarily large number of genes, assay endpoints, and chemicals of interest, available data are sparse, with dose-response curves missing for the vast majority of chemical-gene pairs. Although gene ontologies characterize similarity among genes with respect to known cellular functions and biological pathways, the sensitivity of various pathways to environmental contaminants remains unclear. We propose a novel Dose-Activity Response Tracking (DART) approach to predict the biological activity of chemicals across genes using information on chemical structural properties and gene ontologies within a Bayesian factor model. Designed to provide toxicologists with a flexible tool applicable across diverse HTS assay platforms, DART reveals the latent processes driving dose-response behavior and predicts new activity profiles for chemical-gene pairs lacking experimental data. We demonstrate the performance of DART through simulation studies and an application to a vast new multi-experiment data set consisting of dose-response observations generated by the exposure of HepG2 cells to per- and polyfluoroalkyl substances (PFAS), where it provides actionable guidance for chemical prioritization and inference on the structural and functional mechanisms underlying assay activation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2512_02327 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Leveraging ontologies to predict biological activity of chemicals across genes Kampe, Jennifer N. Dunson, David B. Carberry, Celeste K. Rager, Julia E. Zilber, Daniel Messier, Kyle P. Applications High-throughput screening (HTS) is useful for evaluating chemicals for potential human health risks. However, given the extraordinarily large number of genes, assay endpoints, and chemicals of interest, available data are sparse, with dose-response curves missing for the vast majority of chemical-gene pairs. Although gene ontologies characterize similarity among genes with respect to known cellular functions and biological pathways, the sensitivity of various pathways to environmental contaminants remains unclear. We propose a novel Dose-Activity Response Tracking (DART) approach to predict the biological activity of chemicals across genes using information on chemical structural properties and gene ontologies within a Bayesian factor model. Designed to provide toxicologists with a flexible tool applicable across diverse HTS assay platforms, DART reveals the latent processes driving dose-response behavior and predicts new activity profiles for chemical-gene pairs lacking experimental data. We demonstrate the performance of DART through simulation studies and an application to a vast new multi-experiment data set consisting of dose-response observations generated by the exposure of HepG2 cells to per- and polyfluoroalkyl substances (PFAS), where it provides actionable guidance for chemical prioritization and inference on the structural and functional mechanisms underlying assay activation. |
| title | Leveraging ontologies to predict biological activity of chemicals across genes |
| topic | Applications |
| url | https://arxiv.org/abs/2512.02327 |