Fig. 7: scNiche accurately identifies the zonation patterns from the central vein to the portal node in the normal mouse liver.

a The proportion of each donor in each niche (top) and the enrichment scores of each cell type in each niche (bottom) across 6 normal donors and 4 TD donors. The enrichment scores are calculated among all 15 niches, and the p-value is calculated with the one-sided Mann-Whitney U test (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001). b The cell niches identified by scNiche in tile 2103, tile 2104, and tile 2105, each cell is colored by the niche labels (top) and the cell type labels (bottom). c The proportion of each cell type in Niche 0, 3, 12, 5, 14, 11, and 1. d, The normalized average expression levels of 216 differentially expressed genes (adjusted p-value < 0.05) in Niche 0, 3, 12, 5, 14, 11, and 1. The p-value is calculated with the two-sided Wilcoxon rank-sum test and is adjusted with the Benjamini-Hochberg correction. e The average expression levels of Cyp2e1, Gulo, Hamp, Hamp2, Alb, and Cyp2f2 in Niche 0, 3, 12, 5, 14, 11, and 1. For each niche, only donors with a proportion of that niche exceeding 5% are considered. Data are presented as mean values with a 95% confidence interval. f The gene expression signature scores of Niche 0, 3, 12, 5, 14, 11, and 1 for six different KEGG pathways. Data are presented as mean values with a 95% confidence interval. Source data are provided as a Source Data file.