Possibility and problems of the micro-array technique and cluster analysis in the research on oral carcinoma

Abstract

Recently, comprehensive studies of gene expression in cancer have been made possible by the micro-array technique. However, such studies have not always yielded a comprehensive understanding of genetic phenomena in cancer and too much data may confuse researchers, In searching for the genes responsible for tumor metastasis and/or cisplatin resistance, we have demonstrated micro-array analysis combined with gene cluster analysis. During our studies, we faced difficulties such as the precise amplification of micro-scale mRNA, quality check of mRNA, and control of the labeling difference between Cy3- and Cy5-dUTP. In order to solve these problems, we checked RNA by electrophoresis, optical meters, and Affymetrix Test Chip^TM, and confirmed the array data by quantitative real-time PCR. In the cluster analysis, contamination of poor data and hidden common characters among the samples were critical problems. Pathway analysis and evaluation of the gene function using clinical cases and/or transformation were useful to help detect candidate gene clusters.