Differential expression analysis tells us which genes change between two conditions, but a list of genes is rarely enough on its own. Individual genes are noisy and hard to interpret without a broader framework.
Gene set enrichment analysis asks a different question: are the genes belonging to a known pathway systematically shifted toward the top or bottom of a genome-wide ranked list? This matters because many real biological processes involve coordinated but moderate changes across hundreds of genes rather than a few dramatic ones — exactly the pattern a significance threshold discards. This workflow runs RNA-seq differential expression results against four MSigDB collections using fgsea.