Fig. 3. Genes with a cyclic expression pattern in response to temperature fluctuations. Gene expression profiles are organized by phase shift relative to the temperature cycle in the fluctuating temperature acclimation. Each phase shift cluster was organized with a complete linkage algorithm (Peterson, non-centered; Eisen et al., 1998). Each row represents a single cDNA clone and each column a time point in the acclimation time course. About 40% of the 540 cDNA clones that were differentially expressed have a cyclic expression pattern in response to temperature cycling as determined by cross correlation analysis. For the control daily cycles (26°C) and constant acclimation to 20°C and 37°C, expression patterns are corrected relative to t=0. For the fluctuating temperature treatment, the data are presented relative to t=0 as well as with circadian rhythms subtracted (labeled `The effect of temperature'). Cycling temperature profiles presented with daily rhythms subtracted will have an expression pattern near a 1:1 ratio with controls if there is a negligible effect of temperature on gene expression (see Materials and methods for an expanded discussion). Letters on the right margin of the figure correspond to the line graphs presented in Fig. 4. For non-cyclical gene expression patterns see supplemental Fig. 1.