2.12. Immune infiltration analysis

Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data (ESTIMATE) is a tool used to calculate and estimate the extent of stromal cell and immune cell infiltration in malignant tissues. Calculated immune scores were downloaded from the ESTIMATE database for the TCGA cohort. Patients with GC were divided into two groups based on the median immune score.

The TIMER (https://cistrome.shinyapps.io/timer/) database allows for a comprehensive analysis of the level of infiltration of different immune cells. In this study, TM4SF18 expression was assessed in several cancer types by the “ggpubr” package. The correlation between TM4SF18 and immune cell infiltration in GC was analyzed in TIMER. The “Gene” module allows the study of the relationship between TM4SF18 expression and the level of immune cell infiltration (B cells, CD8⁺ T cells, CD4⁺ T cells, neutrophils, macrophages, and dendritic cells) using the TCGA database. The relationship between TM4SF18 expression and different sets of gene markers in immune cells was also investigated by the “correlation” module. Spearman's correlation and statistical significance were used to assess the relevance of TM4SF18 expression to immune infiltration.