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Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.

Tailored gene array databases: applications in mechanistic toxicology

Tatiana V. Karpinets 1, Brent D. Foy 1,* and John M. Frazier 2

1 Department of Physics, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA and 2 Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433-7400, USA

Received on March 19, 2003 ; revised on July 16, 2003 ; accepted on August 9, 2003
Advance Access Publication January 22, 2004

Motivation: The development of an annotated global database suitable for a wide range of investigations is a challenging and labor-intensive task. Thus, the development of databases tailored for specific applications remains necessary. For example, in the field of toxicology, no annotated gene array databases are now available that may assist in the correlation of changes in gene activity to cellular functions and processes associated with the toxic response.

Results: As an example of a tailored annotated database, an attempt was made to systematize available biological information on genes present on the Affymetrix Rat Toxicology U34 GeneChip, with a focus on how the gene products relate to liver cells and their response to chemical toxins. The information collected was imbedded in a local relational database to analyze data obtained in toxicological gene array experiments with hydrazine–exposed hepatocytes. The advantages and benefits of the tailored database in the biological interpretation of the results are demonstrated.

Availability: The database and gene expression data set are available at http://www.wright.edu/~tatiana.karpinets/

Contact: brent.foy{at}wright.edu

* To whom correspondence should be addressed.


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