Table 1.

List of hub genes used to identify the components of the protein homeostasis system associated with the AD metastable subproteome

Hub genes	Proteins	Known functions
ATP6V1H	V-type proton ATPase subunit H	Clathrin coated endocytosis, formation of endosomes
SH3GL2	Endophilin-A1	Synaptic vesicle endocytosis
SLC9A6	Sodium/hydrogen exchanger 6	Exchange of protons across the membrane of early and recycling endosome
RAB6A	Ras-related protein Rab-6A	Retrograde transport from Golgi to ER, transport from endosome to plasma membrane
CDH13	Cadherin-13	Regulation of endocytosis
RBFOX1	RNA binding protein fox-1 homolog 1	RNA binding protein, regulation of alternative splicing events
CLTA	Clathrin light chain A	Major protein of the polyhedral coat of coated pits and vesicles
NSF	Vesicle-fusing ATPase	SNARE binding, regulation of exocytosis
CNK2	Connector enhancer of kinase suppressor of ras 2	Adaptor protein, regulation of signal transduction
ATL1	Atlastin-1	ER to Golgi vesicle transfer
ENC1	Ectoderm-neural cortex protein 1	Proteasomal ubiquitin-independent protein catabolic process
MYCBP2	E3 ubiquitin-protein ligase MYCBP2	Ubiquitin ligase, protein ubiquitination
FBXL2	F-box/LRR-repeat protein 2	Ubiquitin ligase, protein ubiquitination
RFPL1	Ret finger protein-like 1	Zinc ion binding
RNF128	E3 ubiquitin-protein ligase RNF128	Ubiquitin ligase, ubiquitin-dependent protein catabolic process
TUSC3	Tumor suppressor candidate 3	Magnesium transporter

These hub genes are shown in Fig. 4 and are reported here together with their corresponding proteins and their known functions. The list of hub genes corresponding to the AD metastable subproteome is reported in Dataset S1, Table S7.