DNA microarray-based gene expression studies of the model organism Saccharomyces cerevisiae have yielded a large amount of genome-wide data concerning the cell cycle, various growth conditions and environmental stresses. These observations reveal the extent to which various cellular components share common regulatory patterns. The challenge then turns toward dissecting portions of these transcriptional programs in greater detail. How may we use the existing data and DNA microarrays to rapidly identify specific factors that are responsible for the observed patterns? These results generate additional hypotheses, which then can be tested through direct genetic manipulation and re-examination on a genome-wide scale. Additional data will be presented on how DNA microarrays can be used to probe protein-DNA interactions, and how DNA microarrays may be used to rapidly assay transcriptional programs of organisms for which there exists little or no sequence information.