Table 4 Thirty direct gene-gene interactions and the ranking of each link
From: Relation extraction for biological pathway construction using node2vec
Direct relation no. | Starting entity | Target entity | Ranking (node2vec) | Ranking (co-occurrence) | Ranking (DeepWalk) |
|---|---|---|---|---|---|
1 | INS | INSR | 10/100 | – | – |
2 | INSR | IRS1/IRS | 4/100 | 1/100 | 7/100 |
3 | IRS1/ IRS | PI3K | 1/100 | 3/100 | 1/100 |
4 | INSR | SOCS | 8/100 | 10/100 | 6/100 |
5 | SOCS | IRS1/IRS | 2/100 | 3/100 | 2/100 |
6 | IKK | IRS1/IRS | 2/100 | 2/100 | 2/100 |
7 | JNK | IRS1/IRS | 4/100 | 5/100 | 4/100 |
8 | PKCZ | IRS1/IRS | 6/100 | – | 7/100 |
9 | PKCD/E | IRS1/IRS | 2/100 | 4/100 | 2/100 |
10 | ADIPO | ADIPOR | 1/100 | 1/100 | 1/100 |
11 | AMPKK | AMPK | 1/100 | 1/100 | 1/100 |
12 | INSR | SHC | 38/100 | – | 67/100 |
13 | SHC | GRB2 | 5/100 | 5/100 | 16/100 |
14 | GRB2 | SOS | – | – | – |
15 | SOS | Ras | – | – | – |
16 | Ras | Raf | 4/100 | 6/100 | – |
17 | Raf | MEK1/2 | 1/100 | 5/100 | 4/100 |
18 | MEK1/2 | ERK1/2 | 1/100 | 1/100 | 1/100 |
19 | IRS1/IRS | GRB2 | 4/100 | 4/100 | 4/100 |
20 | PI3K | PDK1/2 | 1/100 | 2/100 | 6/100 |
21 | PDK1/2 | AKT | 3/100 | 4/100 | 5/100 |
22 | AKT | GLUT4 | 4/100 | 4/100 | 4/100 |
23 | PDK1/2 | PKCZ | 1/100 | 1/100 | 1/100 |
24 | PKCZ | GLUT4 | 3/100 | 2/100 | 3/100 |
25 | AKT | mTOR | 1/100 | 1/100 | 1/100 |
26 | TNFA | TNFR1 | 6/100 | 1/100 | 6/100 |
27 | TNFA | TNFR2 | 4/100 | 1/100 | 6/100 |
28 | TNFR1 | TRADD | – | – | – |
29 | TRADD | TNFR2 | – | – | – |
30 | TNFR2 | TRAF2 | – | – | – |
Total number of links captured by node2vec, co-occurrence and DeepWalk | 25 | 22 | 23 | Â | Â |