Figure 3: SCENT identifies single-cell subpopulations of biological significance.

(a) Fitted Gaussian mixture model to the signalling entropies of 1,018 single cells (scRNA-Seq data from Chu et al.) using a logit scale for the signalling entropies (x-axis, log₂[SR/(1−SR)]). Bayesian Information Criterion predicted only two-states: a high energy/entropy pluripotent state (magenta-PS1) and a lower-energy non-pluripotent state (cyan-PS2). Number of cells categorized into each state is indicated in plot. (b) Barplot comparing, for each cell-type, the probability that a cell from this cell population is in the pluripotent (prob(Pl)) or non-pluripotent state (probe(NonPl)). Cell-types include human embryonic stem cells (hESCs), neural progenitor cells (NPCs), definite endoderm progenitors (DEPs), trophoblast cells (TBs), human foreskin fibroblasts (HFFs) and endothelial cells (ECs). (c) Barplot of the corresponding Shannon Index for each cell-population type. (d) Distribution of single-cell numbers between inferred potency states and co-expression clusters, as predicted by SCENT. In brown, we indicate ‘landmark clusters’ which contain at least 5% of the total number of single cells. (e) Distribution of single-cell-types among the seven landmark clusters. (f) Inferred lineage trajectories between the seven landmarks which map to cell-types. Border colour indicates potency state: magenta=PS1, cyan=PS2. (g) Left panel: scatterplot of signalling entropy (SR) vs mRNA expression level of a neural stem/progenitor cell marker, HES1, for all NPCs. NPCs categorized as pluripotent are shown in magenta, NPCs categorized into a non-pluripotent state are shown in cyan. NPCs of high and low HES1 expression (as inferred using a partition-around-medoids algorithm with k=2) are indicated with triangles and squares, respectively. Right panel: corresponding boxplot comparing the differentiation potency (SR) of NPCs with low versus high HES1 expression. P value is from a one-tailed Wilcoxon rank-sum test.