Figure 4

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. [4] (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. [29] (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.