Toxicogenomic software tools | Drug discovery data analysis
Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological mechanisms in animal target organs.
Analyzes dose-response data from microarray experiments. BMDExpress was designed to perform a stepwise analysis on microarray data that combines benchmark dose (BMD) calculations with gene ontology (GO) classification analysis. The combination provides dose estimates at which different cellular processes are altered at a defined increase in risk based on expression levels in the untreated controls.
An integrated platform for toxicogenomics data analysis. Toxygates combines a large microarray dataset with the ability to fetch semantic linked data, such as pathways, compound-protein interactions and orthologs, on demand.
Provides an industry-standardised method to predict the purging of potential mutagenic impurities (PMIs) in a synthetic route based on sound scientific principles. Mirabilis can act as the corporate repository of synthetics schemes, reactions and purge factors facilitating internal collaboration and retention of corporate knowledge. The predicted purge factors are derived from a knowledge of the impurity class as well as other factors which affect purging.
Provides enrichment analysis tools for identifying chemical-associated Gene Ontology (GO), pathway (KEGG and Reactome) and Disease Ontology (DO and DOlite) based on a hypergeometric distribution. ChemDIS is a chemical-disease inference system based on chemical-protein interactions. By integrating the chemical-protein interactions and protein-disease interactions, the diseases associated with a given chemical can be inferred from the chemical-protein-disease relationship. ChemDIS is expected to be a useful chemical-disease inference system for assessing potential risks associated with environmental chemicals.
Provides a familiar virtual desktop. The Human Toxome Collaboratorium is a shared computational environment hosted on third-party cloud services. It was developed in the context of the Human Toxome Project, a consortium that aims to map pathways of toxicity (PoT) and endocrine disruption (ED). This platform includes almost 30 software packages containing a mix of commercial, open source, and internally developed applications used to analyze omics technologies, along with general-purpose utilities and development platforms.
A web-based application for visualizing and graphing BMDExpress output files. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment.