Section: Ecotoxicology & Environmental Chemistry
Topic: Environmental sciences, Genetics/Genomics

DRomics, a workflow to exploit dose-response omics data in ecotoxicology

10.24072/pcjournal.325 - Peer Community Journal, Volume 3 (2023), article no. e90.

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Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page gathers links to all resources related to DRomics, including the two shiny applications.

Published online:
DOI: 10.24072/pcjournal.325
Type: Software tool
Keywords: Dose-response modeling, BenchMark Dose (BMD), Adverse Outcome Pathway (AOP), Mode of Action (MoA), environmental risk assessment, transcriptomics, proteomics, metabolomics, multiomics

Delignette-Muller, Marie Laure 1; Siberchicot, Aurélie 1; Larras, Floriane 1; Billoir, Elise 2

1 Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
2 Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Delignette-Muller, Marie Laure; Siberchicot, Aurélie; Larras, Floriane; Billoir, Elise. DRomics, a workflow to exploit dose-response omics data in ecotoxicology. Peer Community Journal, Volume 3 (2023), article  no. e90. doi : 10.24072/pcjournal.325.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.ecotoxenvchem.100105

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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