association varies by cell-cycle stage. (A) Comparing mean Trep of the top decile (10%) of most-induced versus most-repressed cell cycle-regulated genes reveals that genes highly expressed in G2 replicate early in both Sc and Sp, whereas those highly expressed in M/G1 (Sc) or G1 (Sp) replicate late (error bars represent the standard error). (B) The correlation between Trep and expression levels of known cell cycle-regulated genes was calculated separately for expression levels from each time point of cell cycle-synchronized time courses [27, 28]. An oscillation of the correlation coefficient (Pearson’s r) was observed for both budding yeast (all |r| > 0.107 are significant at P < 0.0025) and fission yeast (all |r| > 0.177 are at P < 0.0025). The approximate cell-cycle phase of each time point is shown [27, 28]. Similar oscillations are observed for other methods of synchronization as well (Additional file 1: Figures S1 and S2). (C) A moving average of Trep is shown for all cell cycle-regulated genes, arranged in order of their time of maximal expression, beginning immediately following mitosis. A similar pattern is observed for both yeast species, with the latest Trep for genes with maximal transcript levels in G1, and the earliest Trep for genes with maximal transcript levels in G2.