Gene Set Enrichment Analysis (GSEA)

GSEA was employed to determine the gene sets, including from KEGG, Gene Ontology (GO), Cancer Hallmarks, and Reactome databases, enriched by a pre-ranked list of all genes, which were sorted by the statistical significance of differential expression defined by DESeq2 analysis. Among 5,160 gene sets in this analysis, 50 were cancer hallmark gene sets, which summarize and represent specific well-defined biological states or processes and display coherent expression ¹⁵, 4,436 were from Biological Process of Gene Ontology (GO(BP)) terms (http://geneontology.org/), and 674 were from Reactome (http://www.reactome.org/). Gene sets with FDR < 0.05 were statistically significant.