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Levels of gene expression are dictated by the rate of messenger RNA synthesis and transcription. Our goal is to discover the necessary elements which regulate transcription in the eukaryote genome. Choosing the yeast genome as a model system, we attempt to identify groups of cell-cycle regulated genes with a common control mechanism. Data from the expression level of 418 cell-cycle dependent genes are clustered according to several distance metrics. We compare the performance of three metrics, namely euclidean distance, correlation, and mutual information. The classifications suggested by these criterion are evaluated against known functional classifications. After identifying candidate groups of co-regulated genes, we will examine the upstream regions using several techniques to isolate the essential components of transcriptional control.