Table 1:

Enrichment results of Alzheimer’s disease (AD) genes using MSigDB gene-sets. The initial AD gene list consists of 61 genes, and those gene-sets with Fisher’s test p-value smaller than 0.05/N_gs, where N_gs is the number of gene-sets within each major collections (h,c2,··· c7), are marked with “Y” under n₁ = 61 column. Those with q-value smaller than 0.05 are marked by Y^q. “pv(corr)” is Bonferonni-corrected p-value which is Fisher’s p-value multiplied by N_gs.“qv” is the q-value. “overlap” is defined as $m/\sqrt{n_1{n}_2}$ which measure the proportion of overlapping genes in the geometric mean of the two gene lists. Three other AD gene lists are used for the same enrichment analysis: n₁ = 58 removes the three autosomal dominant AD (ADAD) genes (APP, PSEN1, PSEN2); n₁ = 48 removes all genes where the associated variant allele is rare (minor allele frequency < 0.01); n₁ = 47 removes all genes where the odds-ratio (OR) of the associated variant is known to be within (0.9, 1.1). A gene-set is marked as “Y*” if p-value is smaller than 0.05/N_allgs where N_allgs = 17484 is the total number of gene-sets in MSigDB. Due to space limitation, gene-sets in gone-ontology collection (c5) are not listed if 0.01 < q-value < 0.05 and p-vale > 0.05/N_gs: 75 for n₁ = 61 AD gene list; 3 for n₁ = 58 list; 17 for n₁ = 48 list; and 39 for n₁ = 47 list.

gene-set	n 1	n 2	m	pv	pv(corr)	qv	overlap	change n1
								61	58	48	47
H: hallmark (Ngs=50)
myogenesis	61	200	7	4.9e-6	2.4e-4	2.4e-4	6.3 %	Y	Y	Y	Y
apoptosis	47	161	4	8.1e-4	4.1e-2		4.6 %				Y
C2: known & curated (Ngs=4762), incl. REACTOME
signaling by NOTCH2/3/4	61	12	4	5.8e-8	2.7e-4	9.1e-5	14.8 %	Y*			Y
nuclear signaling by ERBB4	61	38	5	1.7e-7	8.2e-4	2.1e-4	10.4 %	Y*			Y*
activated NOTCH1 transmits sig. nucleus	61	26	4	1.7e-6	8.0e-3	1.6e-3	10.0 %	Y*			Yq
regulated proteolysis of P75NTR	61	10	3	4.3e-6	2.1e-2	3.5e-3	12.1 %	Y			Y*
signaling by ERBB4	61	87	5	1.1e-5	0.053	6.6e-3	6.9 %	Yq			Y*
nrif signals cell death from the nucleus	61	14	3	1.3e-5	0.062	7.8e-3	10.0 %	Yq			Y
signaling by NOTCH 1	61	68	4	8.2e-5	0.39	0.04	6.2 %	Yq			Y
metastasis down	47	149	5	4.2e-5	0.2	0.025	6%				Yq
C3: motif based (Ngs =836)
STAT6_02	61	251	7	2.1e-5	1.8e-2	0.02	5.7%	Y	Y	Y
C5: gene ontology (GO) (Ngs=5917)
reg. amyloid precursor prot. catabolic proc.	61	11	5	2e-10	1.0e-6	1.0e-6	19.3 %	Y*	Y*	Y*	Y*
membrane protein proteolysis	61	35	5	1.1e-7	6.7e-4	3.3e-4	10.8 %	Y*		Yq	Yq
NOTCH receptor processing	61	16	4	2.1e-7	1.2e-3	4.1e-4	12.8 %	Y*			Yq
cell surface	61	726	13	7.2e-7	4.3e-3	9.8e-4	6.2 %	Y*	Yq	Yq	Y
membrane protein ectodomain proteolysis	61	22	4	8.3e-7	4.9e-3	9.8e-4	10.9 %	Y*
positive reg. cell death	61	602	11	4.8e-6	2.9e-2	4.8e-3	5.7%	Y		Yq	Yq
protein lipid complex	61	40	4	9.9e-6	0.059	8.4e-3	8.1 %	Yq	Y	Y	Y*
beta amyloid metabolic process	61	14	3	1.3e-5	0.077	8.7e-3	10.3 %	Yq			Y
humoral immune response	61	157	6	1.5e-5	0.088	8.7e-3	6.1 %	Yq			Yq
reg. cell death	61	1458	16	1.9e-5	0.11	8.7e-3	5.4%	Yq			Yq
reg. incl. body assembly	61	16	3	2e-5	0.12	8.7e-3	9.6%	Yq	Yq	Yq	Yq
reg. neuron death	61	249	7	2e-5	0.12	8.7e-3	5.7%	Yq		Yq	Yq
cell leading edge	61	345	8	2e-5	0.12	8.7e-3	5.5 %	Yq			Y*
reg. cell, amide metabolic proc.	61	346	8	2.1e-5	0.12	8.7e-3	5.5%	Yq		Yq	Yq
membrane protein intra-domain proteolysis	61	17	3	2.4e-5	0.14	9.6e-3	9.3 %	Yq
positive reg. catalytic act.	61	1495	16	2.6e-5	0.15	9.6e-3	5.3%	Yq			Yq
C7: immunologic expression signature (Ngs = 4872)
CD8 αα vs αβ CD161 high tcell up	61	193	8	2.7e-7	1.3e-3	7.7e-4	7.4 %	Y*	Y*	Yq
early thymic progenitor vs dn3 thymoc. up	61	197	8	3.2e-7	1.5e-3	7.7e-4	7.3 %	Y*	Y	Y*
lps vs heatshock and lps stim mef up	61	194	7	4.0e-6	2.0e-2	6.5e-3	6.4 %	Y	Y*	Yq
ID3 K0 vs WT CD8 t-cell down	58	196	6	3.9e-5	0.19	0.038	5.6%		Yq
untreated vs IL2-treated t-cell up	58	192	6	3.4e-5	0.17	0.038	5.7%		Yq