| Info. | Vol.4 - No.2 (2010.06.20) |
|---|---|
| Title | TOXPO: TOXicogenomics knowledgebase for inferring tox based on POlymorphism |
| Authors | Yunju Jo1 , In Song Koh2 , Hyunsu Bae1 , Moo-Chang Hong1 , Min-Kyu Shin1 & Yang Seok Kim1 |
| Institutions | 1Department of Physiology, College of Oriental Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 130-701, Korea 2 Department of Physiology & Systems Medicine, Hanyang University Medical School, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, Korea |
| 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. |
| Keyword | Toxicogenomics, SNP, Bioinformatics, Systems toxicology, Database |
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