Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA)

The GSVA analysis was performed using “GSVA” package in R. The gene sets using in GSVA analysis were downloaded from GSEA molecular database⁶. T cell immunoreaction and PD1-related immunosuppressive pathways were extracted and used for GSVA analysis. As for GSEA analysis (Mootha et al., 2003; Subramanian et al., 2005), we construct a gemcitabine resistance related gene set by comparing the DEGs between the gemcitabine resistance population and main tumor cell population in GSE 36563 dataset and using genes with p value < 0.05 and | Log2 fold change | > 1. The gemcitabine resistance related gene set was shown in Supplementary Table 4.