DRomics: a turnkey tool to support the use of the dose-response framework for OMICs data in ecological risk assessment

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 modelling 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 several challenges concerning modelling and effect concentration (EC) derivation. Furthermore, handling high-throughput datasets is time-consuming and requires effective and automated processing routines. Thus, we developed a freely available tool (DRomics, available as an R-package and as a web-based service) which, after elimination of molecular responses (e.g. differential gene expressions from microarrays) with no concentration-dependency and/or high variability, identifies the best model for concentration-response curve description. Subsequently, an effect concentration (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 restitutes a table of results that can be directly used to perform ERA approaches. Scenedesmus vacuolatus cultures were exposed for 14 hours to five concentrations of triclosan (0.690, 1.22, 2.15, 3.77 and 6.63µg/L) and one solvent control (final DMSO concentration of 0.1 %) with 5 replicates. After sampling, the RNA was extracted, labelled and hybridised to an Agilent one-color array.