TG-GATEs and DrugMatrix

Processed data was generated using a standard workflow. The CEL files have been normalized using the single-channel array normalization function of the SCAN.UPC library available through Bioconductor. Normalized intensities have been used as an input for the differential expression analysis of microarray data using the very well known limma library available through Bioconductor. The data is then made available on EdelweissData for easy access also via APIs. DrugMatrix is one of the world’s largest toxicogenomic reference resources provided by the National Toxicology Program of the US Department of Health and Human Services. It provides access to the toxicogenomic profiles of over 600 different compounds generated with Affymetrix and Codelink microarrays. While both types of microarray cover liver, kidney, thigh muscles, heart and cultured hepatocytes, the Codelink microarrays additionally cover bone marrow, spleen, intestine and brain. At the moment only the processed data for the Affymetrix platform is available. Open TG-GATEs is a Japanese public toxicogenomic database resulting from two joint government-private sector projects (H14-Toxico-001 and H19-Toxico-001) organized by the National Institute of Biomedical Innovation, National Institute of Health Sciences and multiple pharmaceutical companies. The Japanese Toxicogenomics Project generated gene expression and toxicity data in rats and the primary cultured hepatocytes of rats and humans following exposure to 170 compounds (mainly pharmaceutical products). The follow-up Toxicogenomics Informatics Project discovered over 30 different safety biomarkers using the data and generated additional data for verifying the biomarkers and analyzing their mechanisms.