Fig 2: Correlation of gene expression levels in the Mucosal program with ESCC survival.a Heatmap showing two-sided Spearman correlation coefficients between program scores and proportions of TME compositions as well as T cell function associated scores (hereafter refers to as T cell scores) in tumor samples. P < 0.05 is used as the cutoff value. b Bubble plot showing relationships between mutation status of WES-derived frequently mutated genes and program scores, proportions of TME compositions as well as T cell scores. Compositions that significantly increase or decrease in mutated tumors (two-sided Wilcoxon test, P < 0.05) are indicated by purple or green, respectively. Circle size represents P value. MUT, mutant; WT, wild type. c Associations between program gene expression levels and ESCC survival in Discovery cohort (N = 139) and Validation cohort 1 (N = 94). The significances of genes in two cohorts are indicated by color. Plog-rank < 0.05 (two-sided) is used as the cutoff value. d Kaplan–Meier (KM) curves of Discovery cohort (N = 139) grouped by the mucosal index (MI). e KM curves of Validation cohort 1 (N = 94) grouped by the MI. f Representative images of IHC of the proteins produced by the 3 Mucosal genes in Validation cohort 2. Shown are samples with MI 1 (12-9_A4 and 12-8_B4) and MI 2 (12-4_C4). Scale bar, 50 µm. g KM curves of Validation cohort 2 (N = 226) grouped by the MI. h The relationships between the proportion of epithelial cells expressed AGR2, CXCL17 or MUC20 (total expression >0) and Mucosal score in tumor samples. Two-sided Spearman correlation coefficient and P value are indicated. i Differences in selected pathway activities by GSVA between tumors with high or low expression level of Mucosal genes in Discovery cohort and Validation cohort 1, respectively. Shown are t values from the linear model. P values in (d, e, g) are derived from log-rank tests.