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FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data.

Jessica Ewald1, Othman Soufan2, Jianguo Xia2

  • 1Department of Natural Resource Sciences, McGill University, Montreal, QC H9X 3V9, Canada.

Bioinformatics (Oxford, England)
|August 8, 2020
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Summary

This study introduces FastBMD, a web-based tool for transcriptomics dose-response analysis. It offers a significantly faster and more accessible approach to toxicity testing using benchmark dose modeling.

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Area of Science:

  • Toxicology
  • Bioinformatics
  • Computational Biology

Background:

  • Transcriptomics dose-response analysis is a key method for toxicity testing.
  • Standardized statistical approaches exist but lack efficient, accessible software.
  • Current tools are computationally intensive and require local installation.

Purpose of the Study:

  • To develop a computationally efficient and web-based tool for transcriptomics dose-response analysis.
  • To implement standardized benchmark dose (BMD) modeling methods for transcriptomics data.
  • To provide a comprehensive analytical pipeline from raw data to pathway-level analysis.

Main Methods:

  • Development of FastBMD, a web-based tool utilizing R for transcriptomics BMD analysis.
  • Implementation of a comprehensive pipeline for data processing, normalization, and pathway analysis.
  • Benchmarking against existing software to assess computational efficiency.

Main Results:

  • FastBMD demonstrates >60 times greater speed compared to leading existing software.
  • The tool supports transcriptomics data from 13 diverse species.
  • FastBMD provides an integrated workflow for analyzing gene expression data and exploring pathway-level BMD results.

Conclusions:

  • FastBMD offers a significant advancement in computational efficiency and accessibility for transcriptomics dose-response analysis.
  • The web-based platform democratizes advanced toxicity testing methods.
  • This tool facilitates more rapid and comprehensive toxicological assessments.