Statistical analysis of array expression data as applied to the problem oftamoxifen resistance

Background: Although the emerging complementary DNA (cDNA) array technology holds great promise to discern complex patterns of gene expression, its no velty means that there are no well-established standards to guide analysis and interpretation of the data that it produces. We have used preliminary d ata generated with the CLONTECH Atlas(TM) human cDNA array to develop a pra ctical approach to the statistical analysis of these data by studying chang es in gene expression during the development of acquired tamoxifen resistan ce in breast cancer. Methods: For hybridization to the array, we prepared R NA from MCF-7 human breast ceh tumors, isolated from our athymic nude mouse xenograft model of acquired tamoxifen resistance during estrogen-stimulate d, tamoxifen-sensitive, and tamoxifen-resistant growth. Principal component s analysis was used to identify genes with altered expression. Results and Conclusions: Principal components analysis yielded three principal componen ts that are interpreted as 1) the average level of gene expression, 2) the difference between estrogen-stimulated gene expression and the average of t amoxifen-sensitive and tamoxifen-resistant gene expression, and 3) the diff erence between tamoxifen-sensitive and tamoxifen-resistant gene expression. A bivariate (second and third principal components) 99% prediction region was used to identify outlier genes that exhibit altered expression. Two rep resentative outlier genes, erk-2 and HSF-1 (heat shock transcription factor -1), were chosen for confirmatory study, and their predicted relative expre ssion levels were confirmed in western blot analysis, suggesting that semiq uantitative estimates are possible with array technology. Implications: Pri ncipal components analysis provides a useful and practical method to analyz e gene expression data from a cDNA array, The method can identify broad pat terns of expression alteration and, based on a small simulation study, will likely provide reasonable power to detect moderate-sized alterations in cl inically relevant genes.