Chapter 15 - Representational Difference Analysis: A Methodology to Study Differential Gene Expression

Abstract

This chapter describes representational difference analysis (RDA) as a methodology for examining differential gene expression. Differences in transcript levels in the tissues analyzed are imaged in the representations by relative differences in the abundance of the respective cDNA fragments. cDNA–RDA has been proven to be a powerful tool for the identification of differentially expressed genes in many screens in both eukaryotic and prokaryotic systems. RDA is less prone to produce false positives than differential display and is easier to perform. RDA and arraying techniques are powerful tools for the identification of differential gene expression. Combining them can either produce microarrays that contain exclusively highly relevant probe molecules, focusing on the relevant information that can be gathered from hybridization experiments, or simplify the analysis of global difference products. By increasing the initial cycle number, one could apply RDA to a few nanograms of original material, although with limited success. Also, this process may cause bias and will result in more false-positive fragments.