REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
ADSP - Discovery Cohort Whole Exome Sequencing data	Alzheimer’s Disease Sequencing Project (128)	phs000572.v8.p4; https://www.ncbi.nlm.nih.gov/gap/
ADSP – Extension Cohort Whole Genome Sequencing data	Alzheimer’s Disease Sequencing Project (129)	https://www.niagads.org/adsp/content/home
Post-mortem differential expression data for Alzheimer’s disease	Accelerating Medicines Partnership – Alzheimer’s Disease (130, 131, 132, 133, 134, 135)	https://doi.org/10.7303/syn9702085
Mouse Genome Informatics (MGI) database	Bult et al. (88)	http://www.informatics.jax.org/
Drug-Gene Interaction database (DGIdb)	Freshour et al. (136)	https://www.dgidb.org
STRING protein-protein interaction network	Szklarczyk et al. (44)	https://string-db.org/
HINT protein-protein interaction network	Das et al. (45)	http://hint.yulab.org/
Brain specific protein-protein interaction network	Green et al.(46), Zitnik et al. (47)	http://snap.stanford.edu/ohmnet/
Experimental models: Organisms/strains
D. melanogaster: UAS-Tau	Lasagna-Reeves et al. (49), Bloomington Drosophila Stock Center	BDSC strain#: 51363
D. melanogaster: UAS-Aos:β	Chouhan et al. (50), Bloomington Drosophila Stock Center	BDSC strain#: 33769
Software and algorithms
Python 3.7	Python Software Foundation (137)	https://www.python.org/
GraphWave	Donnat et al. (51)	https://github.com/snap-stanford/graphwave
PolyPhen 2 variant impact scores	Adzhubei et al. (43)	http://genetics.bwh.harvard.edu/pph2/dokuwiki/start
Evolutionary Action variant impact scores	Katsonis et al. (42)	http://lichtargelab.org/software/dashboard/
BCFTOOLS	Danecek et al. (138)	https://samtools.github.io/bcftools/bcftools.html
Eigenstrat	Patterson et al. (139)	https://reich.hms.harvard.edu/software
MAGMA	De Leeuw et al. (68)	https://ctg.cncr.nl/software/magma
GeneEMBED	This study	https://github.com/LichtargeLab/GeneEMBED https://doi.org/10.5281/zenodo.6654182