DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment
- Floriane Larras*Floriane Larras*E-mail: [email protected] (F.L.).Helmholtz-Centre for Environmental Research UFZ, Department of Bioanalytical Ecotoxicology, Permoserstraße 15, 04318 Leipzig, GermanyMore by Floriane Larras,
- Elise BilloirElise BilloirUniversité de Lorraine, CNRS, UMR 7360, LIEC, Laboratoire Interdisciplinaire des Environnements Continentaux, 57070 Metz, FranceMore by Elise Billoir,
- Vincent BaillardVincent BaillardUniversité de Lorraine, CNRS, UMR 7360, LIEC, Laboratoire Interdisciplinaire des Environnements Continentaux, 57070 Metz, FranceMore by Vincent Baillard,
- Aurélie SiberchicotAurélie SiberchicotUniversité de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, FranceMore by Aurélie Siberchicot,
- Stefan ScholzStefan ScholzHelmholtz-Centre for Environmental Research UFZ, Department of Bioanalytical Ecotoxicology, Permoserstraße 15, 04318 Leipzig, GermanyMore by Stefan Scholz,
- Tesfaye WubetTesfaye WubetDepartment of Community Ecology, Helmholtz-Centre for Environmental Research−UFZ, Theodor-Lieser-Straße 4, 06120 Halle, GermanyGerman Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, GermanyMore by Tesfaye Wubet,
- Mika TarkkaMika TarkkaGerman Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, GermanyDepartment of Soil Ecology, Helmholtz-Centre for Environmental Research−UFZ, Theodor-Lieser-Straße 4, 06120 Halle, GermanyMore by Mika Tarkka,
- Mechthild Schmitt-Jansen*Mechthild Schmitt-Jansen*E-mail: [email protected] (M.S.J.).Helmholtz-Centre for Environmental Research UFZ, Department of Bioanalytical Ecotoxicology, Permoserstraße 15, 04318 Leipzig, GermanyMore by Mechthild Schmitt-Jansen, and
- Marie-Laure Delignette-MullerMarie-Laure Delignette-MullerUniversité de Lyon, Université Lyon 1, CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, FranceMore by Marie-Laure Delignette-Muller
Abstract
Omics approaches (e.g., transcriptomics, metabolomics) are promising for ecological risk assessment (ERA) since they provide mechanistic information and early warning signals. A crucial step in the analysis of omics data is the modeling of concentration-dependency which may have different trends including monotonic (e.g., linear, exponential) or biphasic (e.g., U shape, bell shape) forms. The diversity of responses raises challenges concerning detection and modeling of significant responses and effect concentration (EC) derivation. Furthermore, handling high-throughput data sets is time-consuming and requires effective and automated processing routines. Thus, we developed an open source tool (DRomics, available as an R-package and as a web-based service) which, after elimination of molecular responses (e.g., gene expressions from microarrays) with no concentration-dependency and/or high variability, identifies the best model for concentration–response curve description. Subsequently, an EC (e.g., a benchmark dose) is estimated from each curve, and curves are classified based on their model parameters. This tool is especially dedicated to manage data obtained from an experimental design favoring a great number of tested doses rather than a great number of replicates and also to handle properly monotonic and biphasic trends. The tool finally provides restitution for a table of results that can be directly used to perform ERA approaches.
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