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A DATABASE FOR TRACKING REPRODUCTIVE TOXICOGENOMIC DATA
Citation:
Bao, W, J E. Schmid, A K. Goetz, H Ren, AND D J. Dix. A DATABASE FOR TRACKING REPRODUCTIVE TOXICOGENOMIC DATA. Presented at Society for the Study of Reproduction, Vancouver, British Columbia, Canada, August 1-4, 2004.
Description:
A Database for Tracking Reproductive Toxicogenomic Data
Wenjun Bao, Judy Schmid, Amber Goetz, Hongzu Ren and David Dix
Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency,
Research Triangle Park, NC 27711
Reproductive toxicogenomic studies generate an extensive amount of toxicological and genomic data. In the toxicological portion of the study, a substantial quantity of data accumulates from classical endpoints such as histology, development, pharmacokinetics and biochemistry. The largest source of genomics data are DNA microarrays, which generate enormous amounts of information in profiling gene expression. Data storage and management becomes essential and quite a challenge, since these large toxicogenomic data sets are often of various formats and content, and even from different research sites. Thus it is desirable to have a more sophisticated system than notebooks and electronic spreadsheets to manage toxicogenomic data. We developed a reproductive toxicogenomics database (RTD) for our studies based on MIAME-Tox guidelines and a relational database theory. This normalized database stores different types of data produced from both toxicological and genomic studies in a hierarchical fashion (e.g., project data, animal data, animal treatment data; various assay data- histology, developmental landmarks, pharmacokinetics and enzyme assays, microarray data associated sample preparations; and image and data file names). The user-friendly interface provides easy procedures for researchers to add, edit, save, delete, and navigate different records. The database application is designed to link with GeNet for the storage of microarray images and data files, as well as with the complementary analysis package GeneSpring (Silicon Genetics, Redwood City, CA). This tracking database also makes it practical to systematically export microarray data into public databases such as GEO of the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/geo) and ArrayExpress of the European Bioinformatics Institute (http://www.ebi.ac.uk/arrayexpress).
This is an abstract of a proposed presentation and does not necessarily reflect EPA policy.