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

Abstract

Motivation The analysis of dose-dependent effects on the gene expression is gaining attention in the field of toxicogenomics. Currently available computational methods are usually limited to specific omics platforms or biological annotations and are able to analyse only one experiment at a time. Results We developed the software BMDx with a graphical user interface for the Benchmark Dose (BMD) analysis of transcriptomics data. We implemented an approach based on the fitting of multiple models and the selection of the optimal model based on the Akaike Information Criterion. The BMDx tool takes as an input a gene expression matrix and a phenotype table, computes the BMD, its related values, and IC50/EC50 estimations. It reports interactive tables and plots that the user can investigate for further details of the fitting, dose effects and functional enrichment. BMDx allows a fast and convenient comparison of the BMD values of a transcriptomics experiment at different time points and an effortless way to interpret the results. Furthermore, BMDx allows to analyse and to compare multiple experiments at once. Availability and implementation BMDx is implemented as an R/Shiny software and is available at https://github.com/Greco-Lab/BMDx/. Supplementary information Supplementary data are available at Bioinformatics online.

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation

“…A dose-dependent analysis was performed with the strategy implemented in the BMDx tool [ 90 ], to test if bafetinib, 7-hydroxystaurosporine and their combination reduce the viral infection rate in a dose-dependent manner. For the analysis, the benchmark response was set to 10% difference with respect to the controls.…”

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials

“…In addition, our data collection can be easily integrated with other transcriptomics data in the context of a read-across analysis to identify similarities in the molecular alterations induced by the ENMs with other phenotypic entities such as chemicals, drugs, and diseases 44 . Moreover, the data sets that we denoted as class I and II, where exposure at multiple doses are available, can be further analyzed to identify dose-dependent molecular alterations [45][46][47][48] .…”

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation

“…A dose-dependent analysis was performed with the strategy implemented in the BMDx tool (Serra et al, 2020b), to test if bafetinib, 7-hydroxystaurosporine, and their combination, reduce the viral infection rate in a dose-dependent manner. For the analysis, the BMR threshold was set to 10% difference with respect to the controls.…”