Genome-wide profiles of histone acetylation. The levels of H3K9ac (a), H3K14ac (b) and H4K8ac (c) in relation to the levels of core histone H3 (a, b) or H4 (c), genome-wide, are shown. The log2 values of the specific immunoprecipitation of the modified histone were represented in relation to the immunoprecipitation of the core histone (i.e., H3 or H4). For the real-lengths representation (left panels), the profiles were centered on the actual TSS  and the data for each probe corresponded to their real distance from the TSS for each gene, from 1000 bp upstream up to the total transcript length, to a maximum of 3000 bp downstream. Probes were binned to 100 bp. The mean and confidence intervals for the means (t-test, 95% confidence) were plotted. Each experiment compared a ChIP with a histone modification antibody to a control ChIP with a core histone antibody. Genes were divided into quintiles according to their transcript length (right panels).