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

Image processing techniques and wavelet analyses have been applied to the y east 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, the y appear as peaks or troughs in colour maps and contour plots of expression levels. Although apparent in the untreated data, these transitions were id entified and enhanced by convolution of a Laplacian kernel with the express ion 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 t hrough two cell cycles. Time-frequency analyses using wavelet transforms su pport these visualization techniques and lead to the conclusion that, with respect to gene expression, the dominant period is not the cell cycle (90 1 20 min) but, more commonly, the higher frequency 30-40 minute submultiple o f the cycle period.