The DNA microarray has revolutionized cancer research. Now, scientists can obtain a genome-wide perspective of cancer gene expression. One potential application of this technology is the discovery of novel cancer biomarkers for more accurate diagnosis and prognosis, and potentially for the earlier detection of disease or the monitoring of treatment effectiveness. Because microarray experiments generate a tremendous amount of data and because the number of laboratories generating microarray data is rapidly growing, new bioinformatics strategies that promote the maximum utilization of such data are necessary. Here, we describe a method to validate multiple microarray data sets, a Web-based cancer microarray database for biomarker discovery, and methods for integrating gene ontology annotations with microarray data to improve candidate biomarker selection.