Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)

Gene ontology (GO) biological processes (BP) were evaluated separately for up- and downregulated DE lists using clusterProfiler v. 3.12.0 (29), fgsea v. 1.10.0 (30) and org.Hs.eg.db v.3.8.2 annotations. The universe set contained all Entrezid genes (n = 21207) used in DE analyses. The minimum gene set size was 5 and the FDR cutoff was set at 10%. Enriched BP were visualized with dot plots or heat plots. For GSEA ( Figure S3 ), the gene list was constructed using limma’s estimated log₂FC. GO BP and Reactome GSEA were estimated with 5000 permutations and with gene sets containing at least five genes (29, 31, 32).