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Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure for risk assessment. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer (), for visualizing and graphing BMDExpress output files. The application consists of Summary Visualization and Dataset Exploratory tools. Through analysis of transcriptomic datasets of the toxicants furan and 4,4-methylenebis(N,N-dimethyl)benzenamine, we demonstrate that the Summary Visualization Tools can be used to examine distributions of gene and pathway BMD values, and to derive a potential point of departure value based on summary statistics. By applying filters on enrichment P-values and minimum number of significant genes, the Functional Enrichment Analysis tool enables the user to select biological processes or pathways that are selectively perturbed by chemical exposure and identify the related BMD. The Multiple Dataset Comparison tool enables comparison of gene and pathway BMD values across multiple experiments (e.g., across timepoints or tissues). The BMDL-BMD Range Plotter tool facilitates the observation of BMD trends across biological processes or pathways. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment. (c) 2015 Her Majesty the Queen in Right of Canada. Journal of Applied Toxicology published by John Wiley & Sons, Ltd.

We developed BMDExpress Data Viewer, which contains two collections of tools, Summary Visualization Tools and Dataset Exploratory Tools, to visualize and analyze BMDExpress output files. Through two case studies, we demonstrate the capabilities of graphically examining transcriptomic dose-response datasets in a risk assessment context by comparing and observing trends in transcriptomic benchmark doses (BMDs) for biological processes and pathways. Our results illustrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files.