Fig. 3: Differential expression in patients comparing cases to controls, with and without controlling for predicted neutrophil percentage.

Volcano plots of differentially expressed genes, without controlling for predicted neutrophil percentage (a) and with controlling for predicted neutrophil percentage (b) in the design matrix. Genes with a log₂ fold change of >0.1 or <−0.1 and adjusted p value > 0.05 are considered differentially expressed. Genes that are either known PD causal variants or mitochondrial genes are colored purple and orange, respectively. PD causal variants and mitochondrial genes that are differentially expressed are additionally labeled by their gene name. Histograms showing the distribution of significantly differentially expressed neutrophil- and lymphocyte-enriched genes in the differential expression analysis without (c) and with d controlling for predicted neutrophil percentage.