Single Nucleosome Epi-Polymorphisms Figure 3. SNEPs are not associated with transcriptional differences but are enriched at conserved regulatory sites. (A) Display from microarray data directly. Density plots representing the distribution of genes with respect to H3K14 acetylation differences (y-axis) and gene expression differences (x-axis). For every gene, three regions were considered as indicated above the panels. For each region, H3K14ac inter-strain difference was estimated as log(acBY/nucBY)2log(acRM/nucRM) (as defined in legend of Figure 2D), averaged across replicated experiments and across all probes interrogating nucleosomal DNA of the region. Gene expression inter-strain differences are represented by their t-statistic computed from data of Brem et al. [20]. r, Pearson correlation coefficient. A similar picture was obtained when using fold change of expression instead of t- statistics (Figure S10). (B) Display from SNEP locations. For every gene, the fraction of H3K14ac SNEPs correlated to expression was defined as the number of SNEPs acetylated in the strain with highest expression, divided by the total number of nucleosomes in the region. Curves represent the PLoS Genetics | www.plosgenetics.org 6 April 2010 | Volume 6 | Issue 4 | e1000913