Details zur Publikation

Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.1021/acs.est.8b04752
Titel (primär) DRomics: A turnkey tool to support the use of the dose–response framework for omics data in ecological risk assessment
Autor Larras, F.; Billoir, E.; Baillard, V.; Siberchicot, A.; Scholz, S. ORCID logo ; Wubet, T. ORCID logo ; Tarkka, M.; Schmitt-Jansen, M.; Delignette-Muller, M.-L.
Quelle Environmental Science & Technology
Erscheinungsjahr 2018
Department BIOTOX; BZF; BOOEK; iDiv
Band/Volume 52
Heft 24
Seite von 14461
Seite bis 14468
Sprache englisch
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.
dauerhafte UFZ-Verlinkung
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 10.1021/acs.est.8b04752