Date: 2010

Journal: Biochip Journal Volume 4, Issue 2, 2010, Pages 99-104 , Doi: 10.1007/s13206-010-4202-0

2010 | TOXPO: TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism…

Jo, Y.a, Koh, I.S.b, Bae, H.a, Hong, M.-C.a, Shin, M.-K.a, Kim, Y.S.a


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. © The Korean BioChip Society and Springer 2010.

Author keywords

Bioinformatics; Database; SNP; Systems toxicology; Toxicogenomics

Indexed keywords

Engineering controlled terms: Bioinformatics; Database systems; Genes; Rats; User interfaces

Comparative genomics; Data source; Data-base management systems; Database; Genetic polymorphisms; Genome database; Genome-wide association; Human genes; Information sources; Knowledge base; Metabolic disease; Mouse genome; Pharmaceutical industry; Pre-clinical; Side effect; SNP; Toxicogenomics

Engineering main heading: Toxicity

EMTREE medical terms: article; bioinformatics; comparative gene mapping; Comparative Toxicogenomics Database; computer program; dbSNP database; factual database; Genetic Association Database; genetic polymorphism; genetic variability; genomics; information system; Internet; Japan Metabolic Disease Database; knowledge base; Mouse Genome Informatics; NHGRI Genome Wide Association Studies; Rat Genome Database; single nucleotide polymorphism; toxicogenomics; TOXPO database

Species Index: Animalia; Rattus

ISSN: 19760280Source Type: Journal Original language: English
DOI: 10.1007/s13206-010-4202-0 Document Type: Article
Publisher: SpringerOpen
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