Fig. 4

ChromTime predictions associate better with expression changes than boundary movements of peaks called in isolation. a For H3K4me2 in mouse T-cell development [17] ChromTime was applied once with data from all time points (ChromTime ALL), and once with single time points in isolation (ChromTime SINGLE; Additional file 2: Supplementary methods). Time points 1, 2, and 3 correspond to T-cell precursors, 4 and 5 to purified thymocytes. Peaks called by both procedures overlapping annotated TSSs were analyzed for their relationship with gene expression changes. i Left: Comparison of agreement with expression for expansions when applying ChromTime ALL and ChromTime SINGLE for the change between time points 3 and 4. Peak boundaries were sorted in decreasing order of their EXPAND posterior probabilities from ChromTime ALL and compared to sorting them in decreasing order of the difference of peak boundary positions in ChromTime SINGLE peaks with positive differences in boundary positions indicating peaks expanding with time. Each boundary was also ranked by the average gene expression difference of TSSs overlapping its block in decreasing order with positive expression differences indicating gain with time. The cumulative average boundary rank of expression change (y-axis) is shown for the boundary change ranking for ChromTime ALL and ChromTime SINGLE (x-axis). Low Y-values indicate stronger association with expression changes. Black line shows expected average expression change rank. Shaded regions indicate 95% confidence intervals. Plots for other time points can be found in Additional file 1: Figure S5. Right: Analogous to left plots for contract posterior probabilities for ChromTime ALL, increasing order of the difference of boundary change positions for ChromTime SINGLE, and increasing order of expression changes. ii Differences between ChromTime ALL and ChromTime SINGLE values shown in i between time points 3 and 4 as well as for all other pairs of time points. Positive values correspond to boundary ranks for which ChromTime ALL posteriors better associate with gene expression changes than boundary movements of ChromTime SINGLE peaks. Black lines show expected difference of zero between random rankings. b As in a for H3K4me3 in human stem cell reprogramming [24]. Time points correspond to human inducible and immortalized fibroblast-like (hiF-T) cells, hiF-T at 5, 10, and 20 days after induction, and human induced pluripotent stem cells (hIPSC)