Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA m icroarrays and samples from yeast cultures synchronized by three independen t methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperat ure-sensitive mutant. Using periodicity and correlation algorithms, we iden tified 800 genes that meet an objective minimum criterion for cell cycle re gulation. In separate experiments, designed to examine the effects of induc ing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found that th e mRNA levels of more than half of these 800 genes respond to one or both o f these cyclins. Furthermore, we analyzed our set of cell cycle-regulated g enes for known and new promoter elements and show that several known elemen ts (or variations thereof) contain information predictive of cell cycle reg ulation. A full description and complete data sets are available at http:// cellcycle-www.stanford.edu.