Extended Data Fig. 4: Validation of five TIMELASER subtypes.

a, Boxplots showing the percentage of TIMELASER modules across 3 PLC subtypes. (HCC, n = 79 cases, ICC, n = 25 cases, CHC, n = 7 cases). b, Heatmap showing the percentage of CM1–5 across tumours in our cohort and three published scRNA-seq cohorts. c, Expression of signature genes for the five TIMELASER subtypes in 453 published liver cancer bulk RNA-seq data. d, Boxplot showing z-scores of signature genes for five TIMELASER subtypes in different cancer types. Colours represents HCC (orange, n = 369 cases), ICC (green, n = 33 cases) and CHC (purple, n = 51 cases). e, Pie charts showing the proportion of TIMELASER subtypes in c. f, Representative CODEX results showing four different TIMELASER subtypes. For each sample, only six representative antibodies staining are displayed in the figure along with DAPI. Scale bar, 500 μm. g, Validation of TIMELASER by a published spatial transcriptomic study of liver cancer. H&E staining and the corresponding spatial feature plots of different marker genes of cell types are shown in different samples. In a and d, n denotes biologically independent samples. Two-sided Wilcoxon rank-sum test is used. For boxplots, centre line shows median, box limits indicate upper and lower quartiles, and whiskers extend 1.5 times the interquartile range, while data beyond the end of the whiskers are outlying points that are plotted individually. **, P < 0.01; ***, P < 0.001.