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Journal articles
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 challenges concerning detection and modelling of significant responses and effect concentration (EC) derivation. Furthermore, handling high-throughput datasets 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 greatnumber 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.
Cited literature [9 references]
https://hal.archives-ouvertes.fr/hal-02309919
Contributor : Aurélie Siberchicot <>
Submitted on : Wednesday, July 22, 2020 - 5:06:22 PM
Last modification on : Wednesday, October 14, 2020 - 3:41:09 AM
Contributor : Aurélie Siberchicot <>
Submitted on : Wednesday, July 22, 2020 - 5:06:22 PM
Last modification on : Wednesday, October 14, 2020 - 3:41:09 AM
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Larras2018.pdf
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