Fig. 3

IFN-I scores for PD midbrain cell subsets. A An IFN-I score was calculated based on 469 screened ISGs. The threshold value was 0.273, and 3883 cells exceeded it. B The tSNE plot of each cell based on the IFN-I score. High-IFN-I-scoring cells are highlighted with red color. C The tSNE plot based on the IFN-I scores between different groups. D The bar plot showing the percent of High-IFN-I-scoring cells in each cell subset between groups. Of 2639 microglial cells in the PD group, 1352 showed high IFN-I activity, contrasting with 407 of 1165 cells in the control group. For endothelial cells, 649 of 717 in the PD group had high IFN-I activity versus 943 of 1008 in the control group. However, comparing pericytes—180 high IFN-I activity of 572 in the PD group against 209 of 651 in the control. E, F GO and KEGG enrichment analysis of DEGs in high-IFN-I-scoring cells. G PPI analysis (MCODE) of DEGs in high-IFN-I-scoring cells. *p < 0.05; ****p < 0.0001