Characterization of TME

To quantify the relative abundance of each cell infiltration in the GC, we used the single-sample GSEA (ssGSEA) algorithm. The gene sets for analyzing each immune cell type were obtained from the study of Charoentong et al. [48]. The enrichment scores calculated by ssGSEA analysis were utilized to represent the relative abundance of each type of immune cell [49, 50].

To investigate the difference of the biological process in different samples, GSVA analysis was performed using GSVA R packages. GSVA is a gene set enrichment method to estimate the variation in the pathway and biological process activity among different samples in a nonparametric and unsupervised manner [51]. The gene sets about senescence and other biological processes were downloaded from MSigDB of the Broad Institute for running GSVA analysis (Table S1) [52]. In addition, the gene sets that contained genes associated with TME, including the angiogenesis signature [53], antigen processing machinery (APM), DNA damage repair response, EMT, pan-fibroblast TGFβ response signature, and TGFβ pathway, were retrieved from a previous research [21].