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• W2145913417 abstract "Abstract Motivation: In early stage drug development, it is desirable to assess the toxicity of compounds as quickly as possible. 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 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. However, until now, no intuitive user interface has been publically available, making it time consuming and difficult for individual researchers to explore the data. Results: We present Toxygates, a user-friendly integrated analysis platform for this database. Toxygates combines a large microarray dataset with the ability to fetch semantic linked data, such as pathways, compound–protein interactions and orthologs, on demand. It can also perform pattern-based compound ranking with respect to the expression values of a set of relevant candidate genes. By using Toxygates, users can freely interrogate the transcriptome’s response to particular compounds and conditions, which enables deep exploration of toxicity mechanisms. Availability and implementation: Toxygates is freely available to the public at http://toxygates.nibio.go.jp. Contact: johan@nibio.go.jp, kenji@nibio.go.jp or y-igarashi@nibio.go.jp Supplementary information: Supplementary data are available at Bioinformatics online." @default.
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• W2145913417 date "2013-09-17" @default.
• W2145913417 modified "2023-10-04" @default.
• W2145913417 title "Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform" @default.
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• W2145913417 doi "https://doi.org/10.1093/bioinformatics/btt531" @default.
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