Fig. 4

Trajectory analysis uncovers the underlying cell phases and governing gene modules.

a Heatmap showing differentially expressed genes (tradeSeq;⁴⁰P_adj < 0.001, top 1500 based on Wald-statistic) along the maturation trajectory. Cells have been allocated to four distinct phases (P1-P4) and into three distinct gene modules (M1-M3) by hierarchical clustering. The columns of the heatmaps correspond to 100 ordered discrete bins covering the maturation trajectory. The bottom line-annotation shows the distribution of sorted subpopulations along the maturation trajectory (see Fig. 3f) and the bar shows the pseudotime score (see Fig. 3e). b Heatmap summarizing average gene expression per module and phase (from a). c Top-5 enriched gene sets per module from the indicated source pathway databases (hypeR⁴¹ over-representation analysis). d Heatmaps of differentially expressed genes (excerpts from a) associated with selected neutrophil-related functional pathways.