Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA)

GSEA, an analytical method based on the entire gene expression matrix, was conducted to derive the significant differences in biological processes between the IS subtypes. Reference gene sets, “c2. all.v7.5.2. entrez.gmt,” were downloaded from the Molecular Signature Database (Liberzon et al., 2015). P _adj < 0.05 and |normalized enrichment score| > 1 were considered to indicate statistical significance. GSVA, a nonparametric unsupervised analysis method, was used to evaluate different pathways enriched in the different samples. In our study, GSVA was performed using the “GSVA” package (Hänzelmann et al., 2013).