Fig. 5

Features explaining main TSS usage changes upon increased alternative TSS usage levels. a Scatter plot of main TSS expression changes (transition versus prior transition state, log₂, fold change) against distances between the upstream and downstream TSS (log₂, nucleotides). The data presented is for T1 (6h vs 2 h in SPO), T2 (8h vs 6 h in SPO), and T3 (60 min YPD vs 6 h SPO) for a total of 1173 data points. A vertical line indicates the distance of 80 bp between main and upstream alternative TSSs. The Pearson correlation coefficient and its p value are displayed. b Density plots of main TSS expression changes (transition versus prior transition state, log2, fold change). The data was taken from three comparisons representing T1 (6h vs 2 h in SPO), T2 (8h vs 6 h in SPO), and T3 (60 min YPD vs 6 h SPO). The red density plot indicates main and upstream alternative TSSs pairs with < 80 bp distance between them (382 pairs), while the blue plot indicates the pairs with ≥ 80 bp distance between them (791 pairs). Main TSS changes from these two groups follow different distributions (Kolmogovov-Smirnov test, p < 0.05). c Scatter plot of main TSS expression changes (transition versus prior transition state, log₂, fold change) against expression levels of alternative TSS (log₂). Main and upstream alternative TSS pairs selected for alternative TSS which were proximal to the main TSS (< 80 bp), the alternative TSS value after transition was relatively high (≥ 50th percentile), and the main TSS value prior to transition was relatively low (≤ 50th percentile), representing 78 pairs. d Same as a and b, except that the data only includes genes whereby the alternative TSS is distal (≥ 80 bp) to the main TSS, the alternative TSS value after transition is relatively high (≥ 50th percentile) and the main TSS value prior to transition is relatively low (≤ 50th percentile), representing 164 pairs. e Multiple regression explaining fold change of main TSSs during cell-fate changes (Y = log₂) by different variables. The genes chosen for this model fit the criteria in d, representing 164 pairs. The three different explanatory variables are given. The semi-partial correlation coefficients (sr) represent the strength of the linear relationship between Y and the specific explanatory variable that remains after controlling for the effects of the other explanatory variables (i.e., the unique effect). The p values reported in the table are for the unique effects of the explanatory variables