dbZach: An Integrative Toxicogenomic Supportive Relational Database System

Lyle D Burgoon1, Paul C Boutros2, Edward Dere, Shane Doran, Shraddha Pai, Raeka Aiyar, Jigger Vakharia, Rebecca Rotman, Tim Zacharewski
1burgoonl@msu.edu, Michigan State University; 2 Michigan State University

dbZach (http://dbzach.fst.msu.edu) is a Minimum Information About Microarray Experiments (MIAME) supportive toxicogenomic relational database that uses Java-based data mining and visualization tools. The current version indexes large microarray datasets using six functional subsystems (i.e. Clones, Genes, Microarray, and Protocols, Sample Annotation, Toxicology) with three in development (Real-Time Polymerase Chain Reaction (Real-Time PCR), Affymetrix, Pathway, and Promoter). The Microarray, Clones and Genes subsystems relate features spotted on internally developed arrays to gene annotation including gene name, abbreviations, chromosomal locations, and function. The Sample Annotation, Toxicology, and Microarray subsystems relate annotative information about experimental samples and their sources to microarray data, in addition to integrating data from pathology, biochemical assays, clinical chemistry, pathway maps, and real-time PCR, thus facilitating an integrative analysis solution for toxicogenomic studies. dbZach is currently populated with human and mouse data with the incorporation of rat data in the next year. The Java-based data mining and visualization tools facilitate microarray data mining, quality control monitoring, and correlation analyses between microarray and real-time PCR data. The dbZach system is built on Oracle 9i, Java2SE, and Java2EE technologies within a Linux-Windows mixed environment. The dbZach system represents a comprehensive solution to the informatic impediments that toxicologists face regarding microarray data management and the integration of other relevant toxicological, pathological, and chemoinformatic data available from desperate databases. Supported by NIH grants ÝT32 ES07255 ES 04911-12, ES 011271 and ES 011777.