Table 1.
|
Artificial linkage interval |
Random control |
Whole genome |
||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TOP | AUC | FE | MRR | TOP | AUC | FE | MRR | TOP | AUC | FE | MRR | ||
ALL (Lasso) |
Leave one out |
62.47% |
90.86% |
68.09 |
8.90% |
57.42% |
90.78% |
57.42 |
8.34% |
29.34% |
90.21% |
2616.84 |
7.57% |
Ab initio |
61.48% |
90.61% |
67.01 |
10.98% |
56.58% |
90.49% |
56.58 |
8.87% |
27.87% |
89.16% |
2484.89 |
8.09% |
|
ALL (Regular) |
Leave one out |
56.96% |
89.92% |
64.25 |
11.20% |
53.69% |
90.24% |
53.69 |
9.98% |
24.16% |
89.01% |
2154.80 |
8.72% |
Ab initio |
55.47% |
89.52% |
63.74 |
11.60% |
52.64% |
90.02% |
52.64 |
9.65% |
23.11% |
88.16% |
2061.20 |
9.22% |
|
PPI |
Leave one out |
47.41% |
86.08% |
51.66 |
16.94% |
42.07% |
82.23% |
42.07 |
18.05% |
9.87% |
79.78% |
880.31 |
19.46% |
Ab initio |
44.82% |
84.45% |
48.85 |
17.95% |
39.29% |
80.02% |
39.29 |
20.29% |
9.16% |
79.05% |
816.98 |
20.08% |
|
KEGG |
Leave one out |
42.16% |
76.02% |
46.20 |
16.36% |
35.89% |
73.12% |
35.89 |
19.50% |
11.48% |
62.38% |
1023.90 |
12.93% |
Ab initio |
41.02% |
75.19% |
44.91 |
16.52% |
34.20% |
71.31% |
34.20 |
20.10% |
11.20% |
62.20% |
998.93 |
13.01% |
|
GS |
Leave one out |
40.34% |
79.08% |
43.97 |
18.59% |
40.20% |
74.07% |
40.20 |
15.80% |
10.64% |
67.26% |
948.98 |
15.09% |
Ab initio |
40.27% |
78.69% |
43.89 |
18.80% |
38.45% |
72.73% |
38.45 |
16.40% |
10.31% |
66.03% |
919.55 |
15.65% |
|
GE |
Leave one out |
23.25% |
74.30% |
25.34 |
31.15% |
17.44% |
69.04% |
17.44 |
29.51% |
1.75% |
67.61% |
156.08 |
28.79% |
Ab initio |
22.97% |
74.03% |
25.04 |
31.48% |
16.53% |
68.60% |
16.53 |
29.94% |
1.47% |
67.12% |
131.11 |
29.21% |
|
GO | Leave one out |
24.65% |
76.99% |
26.86 |
24.94% |
20.24% |
69.18% |
22.24 |
23.51% |
8.05% |
61.74% |
717.98 |
22.63% |
Ab initio | 24.00% | 76.81% | 26.16 | 25.08% | 20.10% | 68.89% | 20.13 | 23.71% | 7.47% | 61.44% | 666.25 | 22.95% |