Table 3.
Performance comparison with AutoMotif for 48 kinases.
| Kinase | New method | AutoMotif | Kinase | New method | AutoMotif | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACC | P | R | ACC | P | R | ACC | P | R | ACC | P | R | ||
| CDK_group(102) | 0.93 | 0.57 | 0.85 | 0.94 | 0.80 | 0.46 | Abl(48) | 0.92 | 0.67 | 0.25 | 0.89 | 0.00 | 0.00 |
| GSK-3_group(33) | 0.91 | 0.56 | 0.15 | 0.91 | 1.00 | 0.03 | PDK-1(35) | 0.96 | 0.85 | 0.66 | 0.93 | 0.82 | 0.32 |
| PLK1(42) | 0.90 | 0.20 | 0.02 | 0.90 | 0.00 | 0.00 | PKA alpha(31) | 0.94 | 0.92 | 0.39 | 0.92 | 0.83 | 0.15 |
| GRK_group(37) | 0.91 | 0.67 | 0.05 | 0.89 | 0.00 | 0.00 | IKK_group(35) | 0.89 | 0.27 | 0.11 | 0.91 | 0.00 | 0.00 |
| EGFR(61) | 0.92 | 0.66 | 0.34 | 0.88 | 0.00 | 0.00 | CaM-KIIalpha(34) | 0.92 | 0.63 | 0.18 | 0.90 | 0.00 | 0.00 |
| MAPK14(50) | 0.92 | 0.57 | 0.50 | 0.90 | 0.22 | 0.04 | GSK-3beta(52) | 0.91 | 0.63 | 0.10 | 0.90 | 0.20 | 0.02 |
| InsR(45) | 0.92 | 0.60 | 0.36 | 0.83 | 0.60 | 0.07 | CaM-KII_group(55) | 0.92 | 0.63 | 0.18 | 0.92 | 0.89 | 0.15 |
| CK2_group(248) | 0.94 | 0.75 | 0.56 | 0.94 | 0.83 | 0.40 | PKB_group(84) | 0.94 | 0.87 | 0.46 | 0.95 | 0.87 | 0.57 |
| AMPK_group(38) | 0.93 | 0.86 | 0.32 | 0.91 | 1.00 | 0.06 | CDK1(147) | 0.94 | 0.63 | 0.84 | 0.92 | 0.65 | 0.28 |
| MAPKAPK2(34) | 0.92 | 0.62 | 0.24 | 0.90 | 0.00 | 0.00 | CDK2(78) | 0.93 | 0.61 | 0.78 | 0.91 | 0.45 | 0.07 |
| CK1_group(33) | 0.91 | 0.50 | 0.12 | 0.91 | 0.00 | 0.00 | CK2 alpha(127) | 0.94 | 0.77 | 0.52 | 0.93 | 0.73 | 0.32 |
| PKA_group(330) | 0.95 | 0.83 | 0.56 | 0.96 | 0.90 | 0.58 | Lyn(48) | 0.93 | 0.81 | 0.27 | 0.88 | 0.00 | 0.00 |
| PKC alpha(188) | 0.93 | 0.75 | 0.27 | 0.92 | 0.78 | 0.11 | RSK_group(23) | 0.95 | 0.81 | 0.57 | No data | ||
| Syk(51) | 0.94 | 0.75 | 0.53 | 0.86 | 0.30 | 0.07 | DNA-PK(21) | 0.93 | 0.60 | 0.57 | |||
| Fyn(49) | 0.91 | 0.42 | 0.10 | 0.90 | 0.00 | 0.00 | Aurora(55) | 0.93 | 0.81 | 0.31 | |||
| MAPK_group(52) | 0.93 | 0.62 | 0.50 | 0.93 | 1.00 | 0.22 | Met(26) | 0.95 | 0.69 | 0.85 | |||
| MAPK3(88) | 0.94 | 0.68 | 0.69 | 0.95 | 0.88 | 0.55 | PHK_group(21) | 0.92 | 0.67 | 0.29 | |||
| MAPK1(117) | 0.95 | 0.67 | 0.76 | 0.93 | 0.67 | 0.42 | GRK-2(29) | 0.92 | 1.00 | 0.10 | |||
| MAPK8(36) | 0.93 | 0.59 | 0.61 | 0.90 | 0.00 | 0.00 | ROCK_group(23) | 0.92 | 0.67 | 0.26 | |||
| Lck(54) | 0.93 | 0.94 | 0.30 | 0.90 | 0.00 | 0.00 | FGFR1(23) | 0.90 | 0.42 | 0.22 | |||
| PKC_group(236) | 0.93 | 0.76 | 0.26 | 0.93 | 0.85 | 0.24 | PDGFR(21) | 0.94 | 0.83 | 0.48 | |||
| Src(154) | 0.92 | 0.61 | 0.24 | 0.90 | 0.05 | 0.01 | CK1(39) | 0.92 | 0.62 | 0.21 | |||
| IGF1R(31) | 0.92 | 0.69 | 0.58 | 0.84 | 0.50 | 0.09 | CDK5(22) | 0.95 | 0.76 | 0.59 | |||
| ATM(57) | 0.95 | 0.85 | 0.60 | 0.97 | 0.91 | 0.75 | PAK1(28) | 0.91 | 0.60 | 0.11 | |||
ACC, P, and R indicate accuracy, precision, and recall, respectively. The mean accuracy, precision, and recall of the new method for 36 kinases are 0.93, 0.67, and 0.40, respectively while those of AutoMotif are 0.91, 0.47, and 0.17, respectively. The values in brackets represent number of known phosphorylation sites in the reference set. Kinase groups which show better performance in our method compared to AutoMotif are bolded.