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Title (Primary) DRomics: A turnkey tool to support the use of the dose–response framework for omics data in ecological risk assessment
Author Larras, F.; Billoir, E.; Baillard, V.; Siberchicot, A.; Scholz, S.; Wubet, T.; Tarkka, M.; Schmitt-Jansen, M.; Delignette-Muller, M.-L.;
Journal Environmental Science & Technology
Year 2018
Department BIOTOX; BZF; BOOEK; iDiv;
Volume 52
Issue 24
Language englisch;
POF III (all) T42;
Supplements https://pubs.acs.org/doi/suppl/10.1021/acs.est.8b04752/suppl_file/es8b04752_si_001.pdf
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.
ID 21308
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=21308
Larras, F., Billoir, E., Baillard, V., Siberchicot, A., Scholz, S., Wubet, T., Tarkka, M., Schmitt-Jansen, M., Delignette-Muller, M.-L. (2018):
DRomics: A turnkey tool to support the use of the dose–response framework for omics data in ecological risk assessment
Environ. Sci. Technol. 52 (24), 14461 - 14468