Tuning in the transcriptome: basins of attraction in the yeast cell cycle

Image processing techniques and wavelet analyses have been applied to the yeast cell cycle expression microchip data to reveal large-scale temporally coherent structures and high frequency oscillations in mRNA levels through the cycle. Because transitions in expression frequently occur in phase, they appear as peaks or troughs in colour maps and contour plots of expression levels. Although apparent in the untreated data, these transitions were identified and enhanced by convolution of a Laplacian kernel with the expression arrays of the first 4096 genes. Transitions associated with maximum up- or down-regulation of mRNA levels appear as bands at 30-40 min intervals through two cell cycles. Time-frequency analyses using wavelet transforms support these visualization techniques and lead to the conclusion that, with respect to gene expression, the dominant period is not the cell cycle (90-120 min) but, more commonly, the higher frequency 30-40 minute submultiple of the cycle period.