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Open TG-GATEs: a large-scale toxicogenomics database.

Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H - Nucleic Acids Res. (2014)

Bottom Line: 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.Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment.Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database.

View Article: PubMed Central - PubMed

Affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan.

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Related in: MedlinePlus

Open TG-GATEs offers hierarchical access from compound and pathology lists to hematology, biochemical parameters and digitized pathology images. Gene expression data are stored as CEL files, which require software capable of interacting with the Affymetrix data file format. Thus, users will have to convert the primary data into a general-purpose format using various algorithms such as MAS5.0, RMA, etc.
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Figure 1: Open TG-GATEs offers hierarchical access from compound and pathology lists to hematology, biochemical parameters and digitized pathology images. Gene expression data are stored as CEL files, which require software capable of interacting with the Affymetrix data file format. Thus, users will have to convert the primary data into a general-purpose format using various algorithms such as MAS5.0, RMA, etc.

Mentions: Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation Systems (TG-GATEs) (Figure 1) is a toxicogenomics database that stores gene expression profiles and traditional toxicological data derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points. The toxicology data is composed of biochemistry, hematology and histopathology findings with pathology imaging from the in vivo studies and cytotoxicity from the in vitro studies. The 170 compounds include representative known liver- and kidney-injuring pharmaceuticals, compounds and chemicals. These data have been generated and analyzed over the course of the 10-year Japanese Toxicogenomics Project (TGP), which was a joint government–private sector project organized by the National Institute of Biomedical Innovation (NIBIO), the National Institute of Health Sciences (NIHS) and 18 pharmaceutical companies (Figure 2).


Open TG-GATEs: a large-scale toxicogenomics database.

Igarashi Y, Nakatsu N, Yamashita T, Ono A, Ohno Y, Urushidani T, Yamada H - Nucleic Acids Res. (2014)

Open TG-GATEs offers hierarchical access from compound and pathology lists to hematology, biochemical parameters and digitized pathology images. Gene expression data are stored as CEL files, which require software capable of interacting with the Affymetrix data file format. Thus, users will have to convert the primary data into a general-purpose format using various algorithms such as MAS5.0, RMA, etc.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384023&req=5

Figure 1: Open TG-GATEs offers hierarchical access from compound and pathology lists to hematology, biochemical parameters and digitized pathology images. Gene expression data are stored as CEL files, which require software capable of interacting with the Affymetrix data file format. Thus, users will have to convert the primary data into a general-purpose format using various algorithms such as MAS5.0, RMA, etc.
Mentions: Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation Systems (TG-GATEs) (Figure 1) is a toxicogenomics database that stores gene expression profiles and traditional toxicological data derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points. The toxicology data is composed of biochemistry, hematology and histopathology findings with pathology imaging from the in vivo studies and cytotoxicity from the in vitro studies. The 170 compounds include representative known liver- and kidney-injuring pharmaceuticals, compounds and chemicals. These data have been generated and analyzed over the course of the 10-year Japanese Toxicogenomics Project (TGP), which was a joint government–private sector project organized by the National Institute of Biomedical Innovation (NIBIO), the National Institute of Health Sciences (NIHS) and 18 pharmaceutical companies (Figure 2).

Bottom Line: 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.Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment.Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database.

View Article: PubMed Central - PubMed

Affiliation: Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, Osaka 567-0085, Japan.

Show MeSH
Related in: MedlinePlus