Fig. 3

Changes in GATA3 binding and gene expression at predicted H3K4me2 dynamics in T-cell development. a Fold enrichments of cell type-specific and shared peaks of GATA3, which is a master regulator in T-cell development [17], are shown for three sets of blocks with predicted H3K4me2 peaks: 1) blocks with peaks present at all time points whose boundaries hold steady on both sides throughout the whole time course (T1-Tn Steady); 2) blocks with non-contracting peaks whose boundaries expand between at least one pair of consecutive time points and have a peak at the last time point (Tx-Tn Expand); and 3) blocks with non-expanding peaks whose boundaries contract between at least one pair of consecutive time points and have a peak at the first time point (T1-Tx Contract). The first column shows the percentage of bases out of all bases covered by peaks of the set. The last row shows the baseline percentage for each feature out of all bases covered by ChromTime peaks at any time point. Percentages are colored from 0 (white) to 100 (green). Fold enrichments in each column are colored from 1 (white) to the maximum value in the column (red). FLDN1 and ThyDP denote differentiated T-cell precursors and purified thymocytes, which are the first and the last time point, respectively. b Boundaries of predicted H3K4me2 peaks in blocks with at least one predicted non-zero length peak overlapping annotated TSSs were sorted in decreasing order by their posterior probability for EXPAND dynamic (left plots) and CONTRACT dynamic (right plots) at each pair of consecutive time points (Additional file 2: Supplementary methods). Gene expression differences between consecutive time points were calculated as the average difference across all genes with overlapping TSSs for each block. For each posterior rank (x-axis) the plot shows the cumulative average gene expression difference across all peak boundaries with equal or higher posterior probabilities (y-axis). Expanding boundaries associated with increase of gene expression and contracting boundaries associated with decrease of gene expression. Shaded regions correspond to 95% confidence intervals