Fig. 4

Results of trajectory inference, RNA velocity analysis, gene set enrichment analysis, and differential gene expression analysis. a TSNE plots showing the two differentiation trajectories. A larger pseudotime value is indicated by a greener dot color. b Box plot showing the distributions of CytoTRACE scores in different MSC subsets. A CytoTRACE score near 1.0 indicates a lower degree of differentiation, and vice versa. An asterisk indicates that the p value of the Wilcoxon test between the two groups was less than 0.0001. The p value of the Kruskal–Wallis test for all groups was less than 2.2e−16. c TSNE plot showing the distribution of transcriptional activity. A longer arrow indicates stronger transcriptional activity. d Heatmap showing the results of the hallmark gene set enrichment analysis. The rows are gene sets, and the columns are cell subsets. A bluer grid color indicates lower enrichment, and vice versa. The left dendrogram of the heatmap represents the similarity of expression patterns in the different gene sets. An asterisk indicates that the p value was less than 0.05. e Heatmap showing the expression of 37 immune-related differentially expressed genes between FSMSCs and HuMSCs. The rows are genes, and the columns are different groups or clusters. A bluer grid color indicates lower gene expression, and vice versa. The left dendrogram of the heatmap represents the similarity of expression patterns in the genes. Furthermore, the left bar with different colors represents different categories