Fig. 10

Unbiased proteomics reveal differential effects of ApoeCh in 5xFAD versus PS19 mice. a DAPs between 5xFAD vs. WT mice. Log-twofold-change on the x-axis, -log-10 p-value on the y-axis. Proteins with p-value < 0.05 are colored in red (upregulated) or blue (downregulated. b DAPs between PS19 vs. WT mice. c Scatterplot of DAPs from comparisons in a and b. Log-twofold-change values of all proteins with p-value < 0.05 are plotted, with 5xFAD vs. WT comparison on the x-axis and PS19 vs. WT on the y-axis. Correlation coefficient R = 0.68, p < 0.001. d DAPs between 5xFAD;ApoeCh vs. 5xFAD mice. e DAPs between PS19;ApoeCh vs. PS19 mice. f Scatterplot of DAPs from comparisons in d and e. 5xFAD;ApoeCh vs. 5xFAD on x-axis, PS19;ApoeCh vs. PS19 on y-axis. g Pathway analysis of all significantly upregulated proteins in the 5xFAD;ApoeCh vs. 5xFAD comparison. h Pathway analysis of all significantly downregulated proteins in the PS19;ApoeCh vs. PS19 comparison. i Protein–protein interaction (PPI) network of all significantly upregulated proteins in the 5xFAD;ApoeCh vs. 5xFAD comparison. Nodes are colored according to function, including mitochondrial associated (red), ribosome associated (green), and postsynaptic structure proteins (blue). The thickness of the line connecting two nodes indicates the degree of confidence in the prediction of the PPI. j PPI network of all significantly downregulated proteins in the PS19;ApoeCh vs. PS19 comparison