Gene Ontology term enrichment analysis of gene expression changes observed in the TRAMP mouse model of prostate cancer upon treatement with green tea catechins

Abstract

The primary purpose of this study was to examine the effect of green tea on the global gene expression profile in the transgenic adenocarcinoma mouse prostate model for prostate cancer (TRAMP model). The mechanism by which green tea alters gene expression and affects an organism on the cellular level is relatively unknown. We obtained published DNA microarray data from McCarthy et al. (2007, Molecular Oncology 1:196–204). There were three groups of mice in this study: water‐fed wild type C57BL/6 mice (controls), water‐fed TRAMP mice (prostate cancer progressing), and green tea catechin‐fed TRAMP mice (prostate cancer delayed) that were sacrified at three different time points 12, 17, 24 weeks of age, with three biological replicates in each group. Labeled RNA from each mouse was hybridized to an Affymetrix Gene Chip. We reprocessed the data using the dChip software to determine differential gene expression. We then used the GenMAPP and MAPFinder programs to perform Gene Ontology (GO) term enrichment analysis to determine which GO terms were overrepresented in the data that were not reported in the original published work. We would like to gratefully acknowledge Timothy J. Yeatman, Saverio Bettuzzi, and Steve Enkemann for providing us with the complete microarray dataset.