Fig. 2

Cell-cycle, SCENIC, and Pseudotime analyses. A Cell-cycle analysis. Heatmap showing expression levels of cell-cycle-related genes in each cell type. Cells were ordered according to the average expression level of cell-cycle-related genes. The color key from white to red indicated expression levels from low to high. The cell-cycle index of each cell type is shown at the right. B SCENIC results. SCENIC binary regulon activity matrix showing all correlated regulons that were active in at least 1% of all regulons. Each column represents a single cell, and each row represents one regulon. The “regulon” refers to the regulatory network of TFs and their target genes. “On” indicates active regulons; “Off” indicates inactive regulons. Cluster labels correspond to those used in the UMAP plot. Representative transcription factors are highlighted. All cells (C) or individual cell type (D) pseudotime analysis using Monocle 2 for cell transcriptomes. Solid black lines indicate the main diameter path of the minimum spanning tree (MST) and provide the backbone of Monocle’s pseudotime ordering of the cells