Toxygates

Interactive toxicity analysis on a hybrid microarray and linked data platform

Johan Nyström-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3080-3086
Number of pages7
JournalBioinformatics
Volume29
Issue number23
DOIs
Publication statusPublished - Dec 1 2013
Externally publishedYes

Fingerprint

Linked Data
Microarrays
Toxicity
Microarray Data
Hepatocytes
Drugs
Toxicogenetics
Databases
Microarray
Genes
Drug-Related Side Effects and Adverse Reactions
Transcriptome
Semantics
Pharmaceutical Preparations
Gene
Biomarkers
Research Personnel
Kidney
Liver
User Interface

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Nyström-Persson, J., Igarashi, Y., Ito, M., Morita, M., Nakatsu, N., Yamada, H., & Mizuguchi, K. (2013). Toxygates: Interactive toxicity analysis on a hybrid microarray and linked data platform. Bioinformatics, 29(23), 3080-3086. https://doi.org/10.1093/bioinformatics/btt531

Toxygates : Interactive toxicity analysis on a hybrid microarray and linked data platform. / Nyström-Persson, Johan; Igarashi, Yoshinobu; Ito, Maori; Morita, Mizuki; Nakatsu, Noriyuki; Yamada, Hiroshi; Mizuguchi, Kenji.

In: Bioinformatics, Vol. 29, No. 23, 01.12.2013, p. 3080-3086.

Research output: Contribution to journalArticle

Nyström-Persson, J, Igarashi, Y, Ito, M, Morita, M, Nakatsu, N, Yamada, H & Mizuguchi, K 2013, 'Toxygates: Interactive toxicity analysis on a hybrid microarray and linked data platform', Bioinformatics, vol. 29, no. 23, pp. 3080-3086. https://doi.org/10.1093/bioinformatics/btt531
Nyström-Persson, Johan ; Igarashi, Yoshinobu ; Ito, Maori ; Morita, Mizuki ; Nakatsu, Noriyuki ; Yamada, Hiroshi ; Mizuguchi, Kenji. / Toxygates : Interactive toxicity analysis on a hybrid microarray and linked data platform. In: Bioinformatics. 2013 ; Vol. 29, No. 23. pp. 3080-3086.
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