Fig. 2.

Quantitative relationship between histone modification levels and expression. (A) Scatterplot with the predicted expression value in CD4+ T-cells using the full linear model on the x axis and the measured expression value in CD4+ T-cells on the y axis. The shades of blue indicate the density of points; the darker color, the more points. The red line indicates the linear fit between predicted and measured expression (y = 0.99x + 0.02), which are highly correlated (r = 0.77), indicating a quantitative relationship between levels of histone modifications at the promoter and gene expression levels. (B) Comparison of prediction accuracy between all possible one-modification, two-modifications, three-modifications models, and the full model for CD4+ T-cells. Models are sorted by ascending prediction accuracy along the x axis. The best models using only a small subset of modifications almost reach the prediction accuracy of the full linear model. (C) Bar plot showing the frequency of appearance of different histone modifications in best scoring three-modifications models (142 models) for CD4+ T-cells. Best scoring models are defined as reaching at least 95% of prediction accuracy of the full linear model. (D, E) Expression values of genes, which were at least 5-fold up or down regulated in CD36+ and CD133+ cells with respect to CD4+ T-cells, predicted using model parameters trained on data from CD4+ T-cells. The predicted and measured expression values are highly correlated for both CD36+ (D) (r = 0.75; 1,412 genes) and CD133+ (E) (r = 0.63; 1,243 genes) cells. The equations of the regression line for both CD36+ and CD133+ cells (y = 0.43x + 6.04 and y = 0.53x + 6.17, respectively) show a high value of the intercept and a slope different from one due to the fact that the levels of the histone modifications were not normalized across cell types.