Fig. 4

Switch group 1 and 2 genes with activated and deactivated transcriptional states Genes are grouped according to the switch groups. For switch group 1 and 2, genes are ordered within each group according to the first switching timepoints (denoted in red) in increasing order. (a,c) the Viterbi path of active transcriptional state for genes in switch group 1 and 2, (b,d) expression profiles of example genes from switch group 1 and 2. Top: log(TPM+1) expression values in pseudotime order. Middle: Fraction of active cells at each pseudotime window. Cells were split into 26 windows. Bottom: Density plot for log(TPM+1) expression values at each time-ordered cell cluster. X-axis scales are 0-0.75, 0-0.6, 0-0.6, and 0-2 respectively