Extended Data Fig. 4: Proteomics analysis of PLD3-labeled PAAS proteomes in 5XFAD mice.

A. Volcano plot show proteins (represented by their gene names) that passed the statistical cutoffs (yellow dots) in 5XFAD mice. The top 10 proteomic hits with the lowest p-value and highest fold changes are indicated by their gene names in black. The selected known PAAS proteins are labeled as green dots and their gene names in green. The black dots among the yellow ones represent proteins being filtered by the statistical cutoff as shown in Fig. 2b. (See Table S1 for full list of proteomic hits). B. Venn diagram shows shared proteomics hits between AD humans and mice. C. Pathway enrichment analysis of PAAS proteome in 5XFAD mice. The Enrichment Map represents a network of pathways where edges connect pathways with many shared genes. Node color reflects the FDR of each pathway. The theme labels were curated based on the main pathways of each subnetwork. Subnetworks with a minimum of four pathways connected by edges are shown. D. IPA pathway analysis of the PAAS proteome in 5XFAD mice. Top 30 CNS-related signaling pathways are shown. The signaling pathways are summarized as 4 modules. The alluvium plot shows different modules connect to the differentially expressed genes (DEGs) and the DEGs connects to the pathways that they are involved. E. IPA pathways related to the three modules with a p-value less than 0.01 are listed. Heatmaps indicate either the -log₁₀ (p-value) or the z score of each signaling pathway (pathways with a z score in red are predicted to be activated while blue ones are predicted to be inhibited). (A, E) Quantification was performed two-sided.