Gene set enrichment analysis was performed for each cell type that underwent differential expression analysis, using the fgsea R package,99 which uses a preranked list of genes to determine gene sets that are enriched based on the gene rankings. In this case, the log2 fold changes from the differential expression analysis were used as the ranks, and pathways from the Reactome database were used as gene sets. See Supplementary Table 9 for full fgsea results for each cell type. For visualization, the top 30 enriched pathways (based on smallest Benjamini-Hochberg-adjusted p values) in each cell type were selected and hierarchically clustered based on number of genes shared between the pathways. Clustered pathways were then manually labeled into 25 groups.
