Molecular transitions reveal that changes in signaling and cell cycle parameters accompany TF alterations. (A) Pseudo-time axes for transitions between cells that produced CD34⁺ cells but no mature cells in STC, to STC-E (left), STC-NM (middle), and STC-B (right). Areas enclosing the most probable regions (minimum area containing 15% of the total probability density) of cells with these lineage capabilities are indicated. Start and end points were set as the most probable point in the first category and the progenitors of single lineages, respectively. (B-D) Normalized levels of each intracellular marker are shown across 100 bins of pseudo-time in the left plots. Bin values represent the median level of a given marker for all cells within that pseudo-time bin. Single cells, colored based on their most probable lineage outputs, are shown for the 4 markers that differ the most over pseudo-time in the left plots (highest residuals). Solid violet lines indicate best fits for either linear, sigmoidal, or Gaussian regressions (fit selected by using the Bayesian Information Criterion). Fits from 1000 bootstrap replicates of 1% of the total cells are shown as faint violet lines to indicate a probable range. Transitions from cells that produced only CD34⁺ progeny in STC to STC-E are shown in (B), to STC-NM in (C), and to STC-B in (D).