(a) A toy example illustrating the rank statistic used to assess whether the DNA-encoded nucleosome organization of promoters of a given gene set encode a relatively open or relatively closed organization. For each gene, we use the model of the nucleosome sequence preferences to compute the DNA-encoded nucleosome coverage over the nucleosome depleted region of its promoter (left, termed PNDR), and rank all genes by these PNDR scores (middle table, values were arbitrarily chosen for illustration). The rank statistic of each gene set is then obtained by computing the area under the curve (AUC) in a graph that plots the fraction of promoters from the gene set (y-axis) that are above a certain PNDR score versus the fraction of all other promoters above that PNDR score, for all possible PNDR values (three plots on right-end). Plots for three sample gene sets are shown: a gene set with a random AUC rank of 0.5 (top, gray); a gene set whose genes have relatively open nucleosome organizations and thus relatively low PNDR scores (middle, pink); and a gene set whose genes have relatively closed nucleosome organizations and thus relatively high PNDR scores (bottom, yellow). (b) For every gene set from the three categories defined in , shown are its PNDR rank statistic, computed as explained in (a), in both C. albicans (y-axis) and S. cerevisiae. Gene sets from each category are colored as in . The three numbered gene sets from category III in are numbered here as well. (c) Example of an AUC plot for one of the gene sets from (b) (the TCA cycle gene set), in both S. cerevisiae (dashed line), and C. albicans (full line). The promoters of the gene set in this example have relatively high PNDR scores in S. cerevisiae and thus encode relatively closed nucleosome organizations, whereas in C. albicans, they have relatively low PNDR scores and thus encode relatively open nucleosome organizations. For example, only ~5% of the gene sets' promoters have higher PNDR scores than the PNDR score which is exceeded by ~50% of the promoters in C. albicans.