Extended Data Fig. 7: The genomic landscape and molecular characteristics of SP-HI, SP-LI, and SP-PF.
a, Genetic profile and associated clinicopathologic features of 97 HCC patients from SP-HI (n = 36), SP-LI (n = 32) and SP-PF (n = 29) groups in the discovery cohort. b-g, Analysis of bulk RNA-seq of 77 HCC samples from SP-HI (n = 28), SP-LI (n = 28) and SP-PF (n = 21) groups in the discovery cohort. b, Heatmap showed the z-scored estimate scores of stromal cell, immune cell and tumor purity using ESTIMATE deconvolution method. P value was calculated by two-sided Kruskal-Wallis test. c, Heatmap showed the z-scored abundance of different immune and stromal cell populations in SP-HI, SP-LI and SP-PF. MCP-counter deconvolution method. P value was calculated by two-sided Kruskal-Wallis test. d, Bar plot showed the constitution of immune cell populations in SP-HI, SP-LI and SP-PF. CIBERSORT deconvolution method. e, Hallmark pathway enrichment of significantly up-regulated DEGs in SP-HI vs others (left), SP-LI vs others (middle), and SP-PF vs others (right). Over-representation analysis (ORA) with p value adjusted by Benjamini & Hochberg method. f, Volcano plots showed the representative up-regulated DEGs in SP-HI vs others (left), SP-LI vs others (middle), and SP-PF vs others (right). DEGs were defined by two-sided Wald test. P value was adjusted by Benjamini-Hochberg method. g, The predicted molecular subclass of each sample. Two-sided Chi-squared test. For all panels, n denotes biologically independent samples.
