EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information.
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.
Hayes
Kevin R
KR
McArdle Laboratory for Cancer Research, 1400 University Avenue, Madison, WI 53706, USA.
Vollrath
Aaron L
AL
Zastrow
Gina M
GM
McMillan
Brian J
BJ
Craven
Mark
M
Jovanovich
Stevan
S
Rank
David R
DR
Penn
Sharon
S
Walisser
Jacqueline A
JA
Reddy
Janardan K
JK
Thomas
Russell S
RS
Bradfield
Christopher A
CA
D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D008070:Lipopolysaccharides / Q000494:pharmacology; D008099:Liver / Q000187:drug effects / Q000378:metabolism; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D047493:PPAR alpha / Q000819:agonists; D018336:Receptors, Aryl Hydrocarbon / Q000819:agonists; D043922:Toxicogenetics
D008070:Lipopolysaccharides; D047493:PPAR alpha; D018336:Receptors, Aryl Hydrocarbon