Extended Data Fig. 2: Gene expression and tissue preference of 89 TIME cell clusters.
From: Liver tumour immune microenvironment subtypes and neutrophil heterogeneity
a, UMAP plots showing the expression of canonical marker genes for clusters in each major cell population. Normalized expression level was abbreviated as Exp. b, Heatmap showing tissue preferences of clusters in each major cell population revealed by Ro/e. c, Boxplots showing proportions of several tumour-enriched TIME clusters divided by PLC subtypes. *, P < 0.05; **, P < 0.01; ***, P < 0.001. (HCC, n = 79 cases, ICC, n = 25 cases, CHC, n = 7 cases). d, Boxplots showing proportions of several cell clusters associated with virus or cirrhosis. (HBV, n = 57 cases, HCV, n = 6 cases, NBNC, n = 50 cases; cirrhosis, n = 46 cases, non-cirrhosis, n = 67 cases). In c-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.
