BMDx

BMDx performs benchmark dose (BMD) analysis on transcriptomics data to quantify dose-dependent gene expression changes for toxicogenomics studies.

Key Features:

• Input data: Accepts gene expression matrices alongside phenotype tables for dose-response analysis.
• BMD and dose metrics: Computes Benchmark Dose (BMD) values and related metrics such as IC50/EC50 estimations from transcriptomics data.
• Model fitting: Fits multiple dose–response models to gene-level expression data.
• Model selection: Selects optimal models using the Akaike Information Criterion (AIC).
• Multi-experiment and multi-omics support: Enables simultaneous analysis across multiple experiments and omics platforms.
• Comparative analysis: Supports comparison of BMD values across time points and between experiments.
• Functional enrichment: Performs functional enrichment analysis of dose-responsive genes.
• Outputs: Produces tables and plots summarizing model fits, dose effects, and enrichment results.

Scientific Applications:

• Toxicogenomics dose-response assessment: Quantifies dose-dependent transcriptomic changes to inform toxicological evaluation.
• Cross-experiment comparison: Compares BMD values and dose-response behaviors across experiments and time points.
• IC50/EC50 estimation from transcriptomics: Derives IC50/EC50 values from gene expression dose–response curves.
• Pathway-level interpretation: Links dose-responsive genes to pathways and functional categories via enrichment analysis.

Methodology:

Processes gene expression matrices with phenotype tables, fits multiple dose–response models to each gene, computes BMD and IC50/EC50 values, and selects optimal models using the Akaike Information Criterion (AIC).