TOXPO: TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism

Yunju Jo, InSong Koh, Hyunsu Bae, Moo Chang Hong, Min Kyu Shin, Yang Seok Kim

Research output: Contribution to journalArticle

3 Citations (Scopus)

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(TOXicogenomics 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.

Original languageEnglish
Pages (from-to)99-104
Number of pages6
JournalBiochip Journal
Volume4
Issue number2
DOIs
StatePublished - 2010 Jan 1

Fingerprint

Toxicogenetics
Knowledge Bases
Polymorphism
Toxicity
Databases
Genes
Toxicology
National Human Genome Research Institute (U.S.)
Database Management Systems
Rats
Genome
Genetic Databases
Informatics
Information Storage and Retrieval
Genome-Wide Association Study
Metabolic Diseases
Drug Industry
Genetic Polymorphisms
Genomics
Single Nucleotide Polymorphism

Keywords

  • Bioinformatics
  • Database
  • SNP
  • Systems toxicology
  • Toxicogenomics

Cite this

Jo, Yunju ; Koh, InSong ; Bae, Hyunsu ; Hong, Moo Chang ; Shin, Min Kyu ; Kim, Yang Seok. / TOXPO : TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism. In: Biochip Journal. 2010 ; Vol. 4, No. 2. pp. 99-104.
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TOXPO : TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism. / Jo, Yunju; Koh, InSong; Bae, Hyunsu; Hong, Moo Chang; Shin, Min Kyu; Kim, Yang Seok.

In: Biochip Journal, Vol. 4, No. 2, 01.01.2010, p. 99-104.

Research output: Contribution to journalArticle

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