Fig. 2: Proteomic and metabolic analyses identify metabolic rewiring in the ATG5 cKO cerebellum.

a,b, Volcano plot of differentially expressed proteins in WT and ATG5 cKO cerebellum at 1 M (a) and 3 M (b). Red coloured circles mark significantly deregulated proteins at P < 0.05 and log₂(fold change (FC)) of <−0.25, >0.25 (determined by two-tailed t-test). See also Supplementary Data 1. N = 5 mice per genotype. c,d, ShinyGO v0.741-based GO analysis of KEGG terms in the cerebellar proteome (P < 0.05 and log₂FC of <−0.25, >0.25) at 1 M (c) and 3 M (d). e, Venn diagram of commonly upregulated proteins (P < 0.05 and log₂FC of <−0.25, > 0.25) in the 1 M and 3 M ATG5 cKO cerebellum. f,g, Volcano plots of differentially abundant metabolites in WT and ATG5 cKO cerebellum at 1 M (f) and 3 M (g). Red coloured circles mark significantly deregulated metabolites at P < 0.05 and log₂FC of <−0.5, >0.5 (determined by two-tailed t-test). See also Supplementary Data 2. N = 5 mice per genotype. h, MetaboAnalyst-based pathway analysis of significantly upregulated and downregulated metabolites in 3 M ATG5 cKO cerebellum (P < 0.05 and log₂FC of <−0.5, >0.5). i, Relative AA profile in 1 M WT and ATG5 cKO cerebellum (N = 5 mice per genotype). Multiple unpaired two-sided t-tests with linear Benjamini, Krieger and Yekutieli correction. j, Volcano plot of the differentially abundant AAs in 1 M ATG5 cKO cerebellum shown in i. Red coloured circles mark the most upregulated AAs. See also Supplementary Data 3. All graphs show the mean ± s.e.m. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001; ****P ≤ 0.0001.

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