Extended Data Fig. 6: Mutational landscape and GMs of malignant cells.

a, Heatmap showing frequencies of five TIMELASER subtypes across 111 PLC patient samples. Detailed clinical and molecular attributes of individual tumour samples are annotated. P values to the right indicate significant non-random distributions for each attribute. Chi-square test is used for categorical variables. Two-way ANOVA test is used for continuous variables. b, Stacked barplots showing the distribution of cancer types, virus and cirrhosis state across TIMELASER subtypes. Chi-square test. c, Boxplots showing the distribution of tumour purity, CNA and TMB inferred by WES data across TIMELASER subtypes. Two-way ANOVA test is used for comparison of multiple groups. Two-sided Wilcoxon rank-sum test is used for comparison between any two groups. d, Heatmap showing the mutational rate of somatic mutations enriched in different TIMELASER subtypes. e, Barplots showing mutational frequencies of TP53, KRAS, IDH1, and CTNNB1 in different TIMELASER subtypes. Colours represent different TIMELASER subtypes. One-sided Fisher’s exact test. Tests are performed between the denoted TIME subtype (P value colour coded) and a combination of all others. f, Heatmaps showing the eight common gene modules (GMs) extracted from tumour cells. g, Boxplots showing the distributions of signature scores of GMs across tumours stratified into five TIMELASER subtypes. Overhead asterisk is significantly higher than that of subtypes with corresponding asterisk colour. Wilcoxon rank-sum test, two-sided. In c and e, (TIME-IA, n = 13 cases, TIME-ISM, n = 7 cases, TIME-ISS, n = 7 cases, TIME-IE, n = 32 cases, TIME-IR, n = 20 cases). In g, (TIME-IA, n = 18 cases, TIME-ISM, n = 8 cases, TIME-ISS, n = 12 cases, TIME-IE, n = 42 cases, TIME-IR, n = 31 cases). In c, e, and g, n denotes biologically independent patients. 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 < 0.05; **, P < 0.01; ***, P < 0.001.