A linear mixed-effects model, accounting for nesting within animals and tissue sections, confirmed a highly significant negative association between protein intensity and distance from the plaque core for both EFEMP1 (β = -0.53, p < 0.0001) and GALNT10 (β = -0.51, p < 0.0001) (Fig. 4 F-H).
The primary significance threshold was set at FDR < 0.10 based on the following considerations: (1) EFEMP1 (plasma-pQTL OR = 7.96, 95% CI [2.17–29.21]) exhibited borderline significance (FDR = 0.062) under conventional FDR < 0.05 [ 39 ]; (2) Its extreme effect size (OR > 5.0) satisfied our tiered confidence criteria for moderate signals [ 40 , 41 ]; (3) Field standards support FDR < 0.1 for novel biomarker discovery in proteomics [ 42 ]; (4) Empirical validation showed 0% false positive rate at FDR < 0.1 in the negative control analysis.