In the following example, GSEA was performed with KEGG pathway. Figure 2A shows the plotting of GSEA enrichment results to visualize the top five perturbed pathways, i.e., the top five highest absolute values of the normalized enrichment score (NES).9 The NES indicates the shift of genes belonging to a certain pathway toward either end of the ranked list and represents pathway activation or suppression. To further explore the pathway crosstalk effects, we visualized gene expression distribution of core enrichment genes using an UpSet plot (Figure 2B). The result shows that the expression values of genes in the intersection of cell-cycle and DNA-replication pathways are higher than those uniquely belonging to either of the two pathways. These overlapping genes are mainly minichromosome maintenance (MCM) genes, which can potentially serve as biomarkers for tumor diagnosis.21 The intersection of the interleukin-17 (IL-17) signaling pathway and the proteasome pathway is only associated with one gene, interferon-γ (IFN-γ). The IL-17 signaling pathway induces an inflammatory response,22 while IFN-γ regulates proteasome formation.23 These effects ultimately reshape the tumor microenvironment.kk <- gseKEGG(geneList, organism = "hsa")
