Fig. 5: Analysis of mouse gastrulation erythroid data (n = 9, 815 cells).

a Streamline plots of SDEvelo and scVelo (dyn) on the projected UMAP. SDEvelo successfully identified the correct transitions, while scVelo (dyn) estimated messy directions. b Heatmap of the estimated latent time for SDEvelo and scVelo (dyn). SDEvelo accurately estimated latent times that matched the differentiation progression, whereas scVelo (dyn) estimated reversed latent times. c Scatter plots of unspliced and spliced data with trajectories generated by SDEvelo, colored by estimated latent times from SDEvelo. Left panel shows genes with transcriptional boosts, and right panel shows genes with reversed directionality. d Gene expression heatmaps in UMAP space for selected genes. e Expression heatmaps along the estimated latent time from SDEvelo for prioritized genes. The color scheme for the cell type and estimated latent time is the same as in (a) and (b), respectively. f Bubble plot of Gene Ontology (GO) enrichment analysis within the contexts of biological process (BP), cellular component (CC), and molecular function (MF). Bubble size represents the number of genes in each GO term, and gray shadows indicate insignificant GO terms. The enrichment analysis was performed using two-tailed Fisher’s exact test, with p-values adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) method. Source data are provided as a Source Data file. g Dot heatmap of ligand-receptor interactions from cell-cell communication (CCC) analysis. The size of each dot indicates the magnitude of the interaction, and the color of the dots represents permutation-based p-values. Statistical significance was assessed using one-tailed permutation tests (P = 1000 permutations) based on aggregated expression values (using Tuckey’s TriMean), with p-values calculated as the fraction of permuted values exceeding the observed values. Source data are provided as a Source Data file. h Chord chart summarizing the number of interactions between different cell subtypes, with connections between blood progenitors and erythroids highlighted.