Table 3.

Known and unrecognized genes associated with the Alzheimer's disease pathway. The cosine similarities between APP and genes in the full space and the reduced dimensional space obtained from NMF are also presented. (n/a: not applicable)

Gene	PubMed co-citation		Symbol match		Full space		NMF (k = 3)
	# co-citation	Rank	# match	Rank	cos θ	Rank	cos θ	Rank
Known genes associated with the Alzheimer's disease pathway (eight genes)
APP	n/a	-	n/a	-	1.0000	1	1.0000	1
APBB1	0	-	97	1	0.4428	5	0.9989	3
PSEN1	2	1	37	5	0.5018	2	0.9989	3
PSEN2	0	-	18	6	0.4172	6	0.9978	7
LRP1	0	-	12	8	0.2674	10	0.8433	8
A2M	0	-	1	10	0.2350	18	0.7479	9
APOE	0	-	0	-	0.2480	13	0.7142	10
MAPT	0	-	1	10	0.3084	8	0.6649	11
Unrecognized genes associated with the Alzheimer's disease pathway (three genes)
APBA1	0	-	54	4	0.3468	7	1.0000	1
APLP1	0	-	95	2	0.4490	4	0.9989	3
APLP2	0	-	85	3	0.4824	3	0.9989	3