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 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.