To identify cell-type-specific expression signatures, we performed cell-type enrichment analysis using DE genes (FDR < 0.25) from the three brain regions. As a reference gene set for brain cell types, we used the “top ranked cell-type-enriched genes based on human data” as provided by McKenzie et al. [33]. These contain the 1000 most enriched genes in a cell type and cover astrocytes, endothelial cells, microglia, neurons, and oligodendrocytes. Using the R package GeneOverlap (v.1.22.0) [34], we assessed the overlap of AUD-status associated DE genes with markers from the different cell populations. Results were adjusted for multiple testing using the Benjamini–Hochberg method as implemented in GeneOverlap.
