Screenshot for budding yeast CLB1. The figure shows the Gene Details Page for the gene CLB1 (a cyclin). (A) The list of experiments in which the gene is measured. Clicking any of these takes the user to another Gene Details Page with only data from that particular experiment. (B) Expression profile chart. The experiments are normalized and aligned onto a common time-scale (in percent of the cell cycle). The individual phases are marked along the time axis and the computationally determined peaktime is marked by a red dot. (C) Summary of the computational analysis based on all data available for this gene in Cyclebase. ‘Rank’ signifies that this is the 78th most periodic gene in budding yeast, ‘P(per)’ and ‘P(reg)’ are P-values that quantify the significance of periodicity and regulation, respectively, and ‘peaktime’ estimates how far into the cell cycle (from M/G₁) the gene is maximally expressed. (D) Schematic illustration of the peaktime (red dot) and phase duration. The gene CLB1 peaks 63 % into the cell cycle, corresponding to the middle of G₂ phase in budding yeast. (E) Gene aliases and description. (F) Download of data in various formats.(G) Database documentation and download.

Benchmark of methods for identifying cell-cycle regulated genes. For each of the four organisms, a benchmark set was compiled of genes whose promoters are bound by known cell-cycle transcription factors (16,29,30), under the assumption that these genes should be highly overlapping with those that display cell-cycle regulation at the transcriptional level (i.e. periodic expression). The panels show the fraction of a benchmark set retrieved as a function of the number of genes suggested for each individual method (1,2,5–28). Better methods should therefore be towards the upper left corner of the plot. Methods which provide a ranked list of genes are displayed as a line, whereas those that only supply an unranked set of genes appear in the plots as cross mark/plus sign. The black dotted line corresponds to picking genes randomly. In all four organisms, the combined analysis of all data within an organism presented by Cyclebase outperforms all existing methods or suggested sets of periodically expressed genes. In all organisms, the curves eventually display the same slope as the random performance curve (black dotted), indicating that including more genes from this point on yields no enrichment in genes from the benchmark set.