Model-based estimation of lowest observed effect concentration from replicate experiments to identify potential biomarkers of in vitro neurotoxicity

Comparison Of Observation-Based And Model-Based Identification Of Alert Concentrations From Concentration-Expression Data

MOTIVATION

An important goal of concentration-response studies in toxicology is to determine an 'alert' concentration where a critical level of the response variable is exceeded. In a classical observation-based approach, only measured concentrations are considered as potential alert concentrations. Alternatively, a parametric curve is fitted to the data that describes the relationship between concentration and response. For a prespecified effect level, both an absolute estimate of the alert concentration and an estimate of the lowest concentration where the effect level is exceeded significantly are of interest.

RESULTS

In a simulation study for gene expression data, we compared the observation-based and the model-based approach for both absolute and significant exceedance of the prespecified effect level. Results show that, compared to the observation-based approach, the model-based approach overestimates the true alert concentration less often and more frequently leads to a valid estimate, especially for genes with large variance.

AVAILABILITY AND IMPLEMENTATION

The code used for the simulation studies is available via the GitHub repository: https://github.com/FKappenberg/Paper-IdentificationAlertConcentrations.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.