Citation:

Kuo, B., F. Webster, R. Thomas, AND C. Yauk. BMDExpress Data Viewer: A Visualization Tool to Analyze BMDExpress Datasets. JOURNAL OF APPLIED TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, 36(8):1048-1059, (2016).

Impact/Purpose:

We developed the BMDExpress Data Viewer, which contains two collections of tools ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’, to enable visualization and analysis of BMDExpress output files. Through two case studies, we demonstrate the capabilities of graphically examining datasets and selecting biological processes that are sensitive to chemical perturbations, as well as comparing and observing trends in biological processes across multiple experimental conditions. BMDExpress Data Viewer is a useful tool to visualize, explore, and analyze BMDExpress output files.

Description:

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at which biological perturbations occur. 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 visualization and graphical analyses of BMDExpress output files. The software application consists of two main components: ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’. We demonstrate through two case studies that the ‘Summary Visualization Tools’ can be used to examine and assess the distributions of probe and pathway BMD outputs, as well as derive a potential regulatory BMD through the modes or means of the distributions. The ‘Functional Enrichment Analysis’ tool presents biological processes in a two-dimensional bubble chart view. By applying filters of pathway enrichment p-value and minimum number of significant genes, we showed that the Functional Enrichment Analysis tool can be applied to select pathways that are potentially sensitive to chemical perturbations. The ‘Multiple Dataset Comparison’ tool enables comparison of BMDs across multiple experiments (e.g., across time points, tissues, or organisms, etc.). The ‘BMDL-BMD Range Plotter’ tool presents ranges of BMDL and BMD values of biological processes as horizontal bars, and enables the observation of trends between pathways. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore, and analyze BMDExpress output files.

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