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)
From: Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations
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 |