Table 2.

Hub genes common to both AD and aging

Gene symbol	AD					Aging
	Probe set	Assay	p value	Module	Kin	Probe set	p value	Module	Kin	Gene description
ATP5A1	213738_s_at	MMSE	4.17 × 10−2	Light blue	0.67	40096_at	7.44 × 10−5	Blue	0.91	ATP synthase alpha chain, mitochondrial
ATP6V1G2	214762_at	ANOVA	1.52 × 10−3	Light blue	0.85	33033_at	1.50 × 10−4	Blue	0.64	Vacuolar ATP synthase subunit G 2
RAB6A	210406_s_at	MMSE	3.05 × 10−2	Light blue	0.76	622_at	1.58 × 10−4	Blue	0.86	RAB6A, member RAS oncogene family
YWHAZ	200638_s_at	MMSE	3.44 × 10−3	Light blue	0.97	34642_at	1.68 × 10−6	Blue	0.96	14-3-3 protein zeta/delta
CDK5	204247_s_at	MMSE	3.13 × 10−3	Blue	0.63	1206_at	2.28 × 10−4	Blue	0.64	Cyclin-dependent kinase 5
PRKCB1	207957_s_at	ANOVA	2.88 × 10−4	Blue	0.71	1217_g_at	1.66 × 10−5	Blue	0.77	Protein kinase C, beta 1
DICER1	213229_at	CvsM	1.78 × 10−2	Brown	0.75	38764_at	1.33 × 10−2	Brown	0.64	Dicer1, Dcr-1 homolog (Drosophila)
LARP4	212714_at	NFT	6.72 × 10−3	Purple	0.64	35180_at	2.72 × 10−2	Brown	0.73	La ribonucleoprotein domain family member 4

These genes are highly connected in each data set and are highly correlated with the respective phenotype of aging or AD progression; both DICER1 and LARP4 increase expression with increasing AD progression and aging, whereas all the other hubs decrease expression with both phenotypes. The method of measuring probe set significance in AD that led to the lowest p value is presented in the AD assay column (with its associated p value). The aging p value represents the probe set's correlation with age. For both studies, k_in represents the intramodular connectivity, with k_in > 0.6 considered significant. In the CvsM assay, the control and moderate AD samples were compared using a t test.