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Original Article

EDGE: A Centralized Resource for the Comparison, Analysis, and Distribution of Toxicogenomic Information

McArdle Laboratory for Cancer Research, University of Wisconsin-Madison Medical School, Madison, Wisconsin (K.R.H., A.L.V., G.M.Z., B.J.M., J.A.W., R.S.T., C.A.B.); Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin (M.C.); Amersham Biosciences Inc., Sunnyvale, California (S.J., D.R.R., S.P.); Department of Pathology, Northwestern University, The Feinberg School of Medicine, Chicago, Illinois (J.K.R.); and CIIT Centers for Health Research, Research Triangle Park, North Carolina (R.S.T.)

Abstract

Transcriptional profiling via microarrays holds great promise for toxicant classification and hazard prediction. Unfortunately, the use of different microarray platforms, protocols, and informatics often hinders the meaningful comparison of transcriptional profiling data across laboratories. One solution to this problem is to provide a low-cost and centralized resource that enables researchers to share toxicogenomic data that has been generated on a common platform. In an effort to create such a resource, we developed a standardized set of microarray reagents and reproducible protocols to simplify the analysis of liver gene expression in the mouse model. This resource, referred to as EDGE, was then used to generate a training set of 117 publicly accessible transcriptional profiles that can be accessed at http://edge.oncology.wisc.edu/. The Web-accessible database was also linked to an informatics suite that allows on-line clustering and K-means analyses as well as Boolean and sequence-based searches of the data. We propose that EDGE can serve as a prototype resource for the sharing of toxicogenomics information and be used to develop algorithms for efficient chemical classification and hazard prediction.

Address correspondence to: Dr. Christopher A. Bradfield, McArdle Laboratory for Cancer Research, 1400 University Ave., Madison, WI 53706. E-mail: bradfield{at}oncology.wisc.edu

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