Fig. 3

Differential expression of a gene or transcript between cell populations. The top row labels the specific gene or transcript, as is also done in Fig. 6. A difference in mean gene expression manifests in a consistent difference of gene expression across all cells of a population (e.g., high vs. low). A difference in variability of gene expression means that in one population, all cells have a very similar expression level, whereas in another population, some cells have a much higher expression and some a much lower expression. The resulting average expression level may be the same, and in such cases, only single-cell measurements can find the difference between populations. A difference across pseudotime is a change of expression within a population, for example, along a developmental trajectory (compare Fig. 1). This also constitutes a difference between cell populations that is not apparent from population averages, but requires a pseudo-temporal ordering of measurements on single cells