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Updated: Dec 30, 2025

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data.

Angela Serra^1,2, Laura Aliisa Saarimäki^1,2, Michele Fratello^1,2

¹Faculty of Medicine and Health Technology, Tampere University, Tampere 33100, Finland.

Bioinformatics (Oxford, England)

|January 18, 2020

Summary

This summary is machine-generated.

We developed BMDx, a new software for analyzing gene expression data. This tool helps researchers understand dose-dependent effects in toxicogenomics by analyzing multiple experiments simultaneously.

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Area of Science:

Toxicogenomics
Computational Biology
Bioinformatics

Background:

Dose-dependent gene expression analysis is crucial in toxicogenomics.
Existing computational methods have limitations in analyzing omics data and single experiments.

Purpose of the Study:

To develop a user-friendly software tool for Benchmark Dose (BMD) analysis of transcriptomics data.
To enable the analysis of dose-dependent effects across multiple experiments and time points.

Main Methods:

Developed BMDx, an R/Shiny software with a graphical user interface.
Implemented model fitting with Akaike Information Criterion for optimal model selection.
Input: gene expression matrix and phenotype table; Output: BMD, IC50/EC50 estimations, interactive plots.

Main Results:

BMDx facilitates the computation of BMD and related values for transcriptomics data.
The software provides interactive visualizations for detailed investigation of dose effects and functional enrichment.
Enables efficient comparison of BMD values across different time points and multiple experiments.

Conclusions:

BMDx offers a fast and convenient approach for interpreting dose-dependent gene expression data.
The tool enhances the analysis of toxicogenomic studies by allowing multi-experiment comparisons.
BMDx is available as open-source software for the scientific community.