TOXPO: TOXicogenomics knowledgebase for inferring toxicity based on POlymorphism

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 informati...

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Bibliographic Details
Published in:Biochip journal 2010-06, Vol.4 (2), p.99-104
Main Authors: Jo, Yunju, Koh, In Song, Bae, Hyunsu, Hong, Moo-Chang, Shin, Min-Kyu, Kim, Yang Seok
Format: Article
Language:English
Subjects:
Biomedical Engineering and Bioengineering
Biotechnology
Chemistry
Chemistry and Materials Science
Clinical trials
Data base management systems
Gene polymorphism
Genome-wide association studies
Genomes
Genomics
Informatics
Information management
Information retrieval
Information sources
Knowledge bases (artificial intelligence)
Metabolic disorders
Original Research
Pharmaceutical industry
Polymorphism
Side effects
Single-nucleotide polymorphism
Toxic diseases
Toxicity
Toxicology
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Summary: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 .
ISSN:1976-0280
2092-7843
DOI:10.1007/s13206-010-4202-0