Fig. 6: Cell-type-specific transcriptomic variation along the liver zonation revealed by STEM.

a Distribution of zonation scores on the ST data. A high score indicates the CV region, while a low score indicates the PV region. Arrow in red indicates the direction from a low (PV) to a high (CV) zonation score region. b Illustration of the transfer of zonation scores from ST to SC data. The zonation scores of SC data are obtained by multiplying the SC-ST mapping matrix with the ST zonation score vector. Then cells are grouped into different cell types, and the analysis of cell-type-specific gene variation along the axis can be performed. c Expression profiles of six zonation landmark genes along the PV-CV axis. The x axis represents the zonation score, and the y-axis represents the gene’s raw count expression level. Each curve was obtained by fitting the polynomial function of degree 3 on the corresponding expression value. d Heatmap of the top significantly differentially expressed genes along the PV-CV axis. Gene expression values are scaled, with red indicating high expression and blue indicating low expression. e Expression profiles of six endothelial cell-specific marker genes along the PV-CV axis. The top and bottom genes are highly expressed in the PV and CV regions, respectively. The shading shows the 95 confidence interval. f Violin plots of fibroblast-specific marker genes identified by STEM. The top panel shows the PV marker gene, while the bottom panel shows the CV marker gene.