Fig. 4: Identification of transition genes and their function at E10.5. | Nature Communications

Fig. 4: Identification of transition genes and their function at E10.5.

From: Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development

Fig. 4

a CellRank UMAP plot directed by RNA velocity and cell-cell similarity for clusters C2, C3, C4, and C10 from the feature plot in Fig. 3a. b UMAP plot for cell fate probabilities of CNCCs differentiating towards smooth muscle cells. c Directed PAGA plot of NCCs. Pie charts show summarized fate probabilities of individual clusters, with blue representing the proportion of cells in each cluster with high probability to become smooth muscle CNCCs of a cluster, C10. d Heatmap from CellRank showing the expression of selected genes whose expression correlates with transitions of CNCCs fate probabilities, with cells ordered by smooth muscle fate probabilities as latent time (see Supplementary Data 5 for a full list of genes), Asterisk (*) marks newly identified genes connected to CNCCs. e UMAP plots showing expression of marker genes in CNCCs. f GO enrichment analysis of four groups of genes between Bmp4 and Gata6 (defined by their pseudotime; Supplementary Data 6). Example of genes for each selected GO: biological processes are provided. The size of the dots indicates the adjusted p value by Bonferroni and Hochberg correction (Hypergeometric test); adjusted p value are indicated in Supplementary Data 6.

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