Use of three-color cDNA microarray experiments to assess the therapeutic and side effect of drugs

A novel microarray strategy, three-color cDNA microarray experiment, is originally applied to assess drug effects on gene expression patterns of “target disease.” By adding Alexa 594 as a dye-label for the third target sample, it is made possible to monitor changes in gene expression in response to disease and generate clues to gene function with therapeutic intervention only on one array. A new kind of graph, hexaMplot, is constructed to illustrate the meaningful expression patterns of normal-disease-drug in three-color experiment. The therapeutic and side effect of drugs can be understood and indicated by the different regions of hexaMplot. And the testing of correlation coefficient is explored as a statistical tool of the assessment. Such a methodology may prove useful in shortening the cycle, reducing the cost, and improving the efficiency of drug discovery and development.