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BMDExpress Data Viewer - a visualization tool to analyze BMDExpress datasets.

Byron Kuo1, A Francina Webster1,2, Russell S Thomas3

  • 1Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada, K1A 0K9.

Journal of Applied Toxicology : JAT
|December 17, 2015
PubMed
Summary
This summary is machine-generated.

A new web application, BMDExpress Data Viewer, enhances toxicogenomic risk assessment by improving visualization and analysis of benchmark dose (BMD) modeling results. This tool aids in identifying key biological perturbations and deriving critical exposure thresholds.

Keywords:
4,4′-methylenebis(N,N-dimethyl)benzenamine (MDMB)BMDExpressbenchmark dose (BMD)bioinformaticsdata visualizationdose-responsefurangene expressiongenomicshuman health risk assessmentmicroarraytranscriptomics

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Area of Science:

  • Toxicogenomics
  • Computational Toxicology
  • Risk Assessment

Background:

  • Regulatory agencies utilize benchmark dose (BMD) modeling for risk assessment.
  • BMDExpress software analyzes transcriptomic data to identify transcriptional BMDs.
  • Existing BMDExpress software has limitations in graphing, analysis, and output interpretation.

Purpose of the Study:

  • To develop a web-based application, BMDExpress Data Viewer, for enhanced visualization and analysis of BMDExpress output files.
  • To provide tools for exploring gene and pathway BMD values, functional enrichment, and multi-dataset comparisons.
  • To facilitate the application of toxicogenomics in risk assessment by improving data interpretation.

Main Methods:

  • Development of a web-based application with "Summary Visualization" and "Dataset Exploratory" tools.
  • Utilized transcriptomic datasets for toxicants furan and 4,4'-methylenebis(N,N-dimethyl)benzenamine.
  • Incorporated filtering capabilities for enrichment P-values and significant gene counts.

Main Results:

  • The "Summary Visualization Tools" enable examination of gene and pathway BMD value distributions.
  • "Functional Enrichment Analysis" tool identifies perturbed biological processes and related BMDs.
  • "Multiple Dataset Comparison" and "BMDL-BMD Range Plotter" tools facilitate cross-experiment analysis and trend observation.

Conclusions:

  • BMDExpress Data Viewer is a valuable tool for visualizing, exploring, and analyzing BMDExpress output.
  • The application aids in rapid assessment of data quality, model fit, and sensitive pathway perturbations.
  • Enhanced data visualization supports the application of toxicogenomics in regulatory risk assessment.