BioChip Journal

, Volume 4, Issue 2, pp 99–104

TOXPO: TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism

  • Yunju Jo
  • In Song Koh
  • Hyunsu Bae
  • Moo-Chang Hong
  • Min-Kyu Shin
  • Yang Seok Kim
Original Research

DOI: 10.1007/s13206-010-4202-0

Cite this article as:
Jo, Y., Koh, I.S., Bae, H. et al. BioChip J (2010) 4: 99. doi:10.1007/s13206-010-4202-0

Abstract

Recently, many state-of-the-art omics technologies are being applied to systems toxicology research because evaluation of toxicity in pre-clinical trials is a big issue in the pharmaceutical industry. Now, genetic polymorphisms are also considered in systems toxicology because polymorphism information can be used to explain individual-specific toxicity and/or side effects. However, in spite of its importance, no well-organized database for individual toxicity has been reported to date. To address this issue, we first extracted toxicity-related human gene information from the CTD, and then, using comparative genomics techniques and retrieving information from animal databases, we gathered the corresponding genes from the mouse and rat. The CTD (Comparative Toxicogenomics Database), dbSNP, RGD (Rat Genome Database), MGI (Mouse Genome Informatics), NHGRI Genome-Wide Association Studies, JMDBASE (Japan Metabolic Disease Database) and GAD (Genetic Association Database) were used as original information sources. The dbSNP was used as a major polymorphism data source, and other related databases were also used to find disease- and/or toxicity-related SNPs. The MSSQL server was used as a database management system and ASP was used to construct a database-web interface. The result of our efforts is TOXPO(TOXico-genomics knowledgebase for inferring toxicity based on POlymorphism), the first database managing toxicogenomics information based on genomic variation. This database is freely available on website http://163.180.41.43/toxpo.

Keywords

Toxicogenomics SNP Bioinformatics Systems toxicology Database 

Copyright information

© The Korean BioChip Society and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Yunju Jo
    • 1
  • In Song Koh
    • 2
  • Hyunsu Bae
    • 1
  • Moo-Chang Hong
    • 1
  • Min-Kyu Shin
    • 1
  • Yang Seok Kim
    • 1
  1. 1.Department of Physiology, College of Oriental MedicineKyung Hee UniversityDongdaemun-gu, SeoulKorea
  2. 2.Department of Physiology & Systems MedicineHanyang University Medical SchoolSeongdong-gu, SeoulKorea