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

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 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.

ORGANISM(S): Scenedesmus vacuolatus

PROVIDER: GSE122159 | GEO | 2019/03/01

REPOSITORIES: GEO