Table 1. Reactome pathways identified as significant in AD phospho-proteome for 3/6/9 month time points.

Each row corresponds to a different pathway. Up to seven significant pathways are shown for each time point. “# of proteins” column indicates the number of proteins in the pathway, the first number is for proteins identified in our data and the second one (after /) is for total number of proteins.

	Pathway	# of Proteins	Z-Score	FDR
3 Month	Regulation of gap junction activity	2 / 3	4.60	0.0019
	Cation-coupled Chloride cotransporters	2 / 7	4.13	0.0053
	RHO GTPases activate PAKs	10 / 20	3.34	0.08
	DARPP-32 events	7 / 16	3.31	0.08
	RAF/MAP kinase cascade	26 / 91	−4.28	0.004
6 Month	Regulation of gap junction activity	2 / 3	3.59	0.021
	Scavenging by Class A Receptors	2 / 7	8.64	0
	EPH-ephrin mediated repulsion of cells	5 / 30	4.90	0.00021
	Noncanonical activation of NOTCH3	2 / 5	4.62	0.00054
	Nuclear signaling by ERBB4	2 / 9	4.21	0.0028
	NRIF signals cell death from the nucleus	2 / 10	4.10	0.029
	CS/DS degradation	2 / 7	−3.37	0.0033
9 Month	Regulation of gap junction activity	2 / 3	5.41	1.4e-05
	Scavenging by Class A Receptors	2 / 7	5.66	6.4e-06
	Insertion of tail-anchored proteins into the endoplasmic reticulum membrane	4 / 12	4.83	0.00015
	MTOR signaling	5 / 14	3.71	0.006
	Norepinephrine Neurotransmitter Release Cycle	8 / 15	−4.10	0.0017
	Dopamine Neurotransmitter Release Cycle	13 / 20	−4.25	0.0015
	GABA synthesis, release, reuptake and degradation	8 / 12	−4.74	0.00018