Extended Data Fig. 3: Clusters, signatures, and prognosis of five TIMELASER subtypes.
From: Liver tumour immune microenvironment subtypes and neutrophil heterogeneity
a, Heatmap showing frequencies of TIME cell clusters in 5 CMs. b, Forest plot showing the clinical relevance of clusters in each CM revealed by log10(hazard ratio) based on PFS. Cox regression. Log-rank test. c, Dot heatmap showing enriched pathways across TIMELASER subtypes. Benjamini–Hochberg-adjusted hypergeometric test. d, Boxplots showing the expression of given signatures in different TIMELASER subtypes. Signature scores of TIMELASER subtypes with overhead asterisk are significantly higher than that of subtypes with corresponding asterisk colour. Wilcoxon rank-sum test, two-sided. (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, 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. e, Overall survival (OS) with each patient assigned to a single CM. Log-rank test. f, OS of cases stratified by each TIMELASER module. Log-rank test. In b and d, *, P < 0.05; **, P < 0.01; ***, P < 0.001.
