1.2. Toxicogenomics dataset

1.2. The TG-GATEs toxicogenomics dataset

The data in the tutorial is from the Japanese Toxicogenomics Project (TGP) database and from the compound acetaminophen, a ToxBank/SEURAT-1 reference compound.

Biomarker genes can help predict whether a candidate drug will adversely affect a given individual, but they are often difficult to discover. In addition, the mechanism of toxicity of many drugs and common compounds is not yet well understood. The Japanese Toxicogenomics Project (TGP) provides a large database of systematically collected microarray samples from rats (liver, kidney, and primary hepatocytes) and human cells (primary hepatocytes) after exposure to 170 different compounds in different dosages and at different time intervals. The TGP project (Uehara, et al., 2010) that performed over 25000 microarray-based toxicogenomics assays, began in 2002 as a joint government-private sector project. This project lasted for 10 years, ending in 2012. The human in vitro liver dataset that we are using contains 2605 arrays, of which we have selected 24 as an example.

In early 2011, most of the TGP data, including the gene expression, biochemical, blood and histopathological data, as well as high resolution images of in vivo organ samples, was released to the public through the Open TG-GATEs (OTG) website (http://toxico.nibio.go.jp).

Link to the The basics on Toxicogenomics video Tutorial.

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