Correlation between expression level and H3K4me3/H3K27me3 occupancy at bivalent genes in embryonic stem (ES) cells. (a) Box plot showing 25th, 50th and 75th percentiles of H3K4me3/H3K27me3 ratio for 1,843 bivalent genes associated with 3 different expression levels, as calculated by Pan et al.  (above the mean value for all expressed genes; between the mean value and 1; and below 1). The error bars represent 1.5 times the interquartile range above and below the median. Outliers are plotted individually. The mean of each population is shown as a black cross. Statistical differences were determined using a two-tailed unpaired Student's t test. (b) A total of 1,844 bivalent genes were ranked according to their levels of expression (low to high, x axis) and plotted against the moving average (window size 100 genes, step 1) of the ratios of H3K4me3/H3K27me3 (y axis). Spearman's r value is shown in the graph. (c) Scatterplot showing the H3K4me3/H3K27me3 ratio for 23 bivalent genes associated with 3 different expression patterns as shown by Gibson et al.  (present in all the cells analysed, present sporadically in some but not all cells, and absent). The mean of each population is shown as a black bar. The H3K4me3/H3K27me3 ratio has been calculated from the signal derived from the number of H3K4me3 and H3K27me3 sequence reads in an area spanning from -3 kb to +3 kb around the transcription start site (TSS). Statistical analysis made with different windows (from -4 kb to +1 kb and from -0.5 kb to +2 kb) gave similar results.