Table 2 Cross-validation evaluation of sequence and structure-based phosphorylation site predictions on 3D structures.
Kinase group | Number of positive data | Number of negative data | Sequence-only | Structural information | Combination of sequence and structural information | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Sn | Sp | Acc | Sn | Sp | Acc | Sn | Sp | Acc |
Phosphorylated Serine (pSer) | |||||||||||
All serine data | 1554 | 3108 | 61.4% | 62.0% | 61.8% | 66.9% | 68.1% | 67.7% | 72.9% | 71.1% | 71.7% |
CDK | 11 | 22 | 72.7% | 81.8% | 78.8% | 90.9% | 86.8% | 87.9% | 90.9% | 86.8% | 87.9% |
CK1 | 10 | 20 | 20.0% | 90.0% | 66.7% | 100% | 95.0% | 96.7% | 100% | 95.0% | 96.7% |
CK2 | 24 | 48 | 66.7% | 87.5% | 80.6% | 87.5% | 87.5% | 87.5% | 91.7% | 89.6% | 90.3% |
MAPK | 17 | 34 | 52.9% | 94.1% | 80.4% | 76.5% | 97.1% | 90.2% | 82.4% | 97.1% | 92.2% |
PIKK | 15 | 30 | 26.7% | 83.3% | 64.4% | 80.0% | 86.7% | 84.4% | 73.3% | 83.3% | 80.0% |
PKA | 56 | 112 | 79.1% | 78.8% | 78.9% | 83.6% | 84.3% | 84.1% | 89.1% | 91.4% | 90.7% |
PKB | 12 | 24 | 75.0% | 66.7% | 69.4% | 75.0% | 83.3% | 80.6% | 83.3% | 83.3% | 83.3% |
PKC | 50 | 100 | 77.3% | 78.0% | 77.8% | 81.2% | 80.0% | 80.4% | 85.3% | 86.0% | 85.8% |
PKG | 10 | 20 | 80.0% | 80.0% | 80.0% | 80.0% | 85.0% | 83.3% | 80.0% | 85.0% | 83.3% |
PLK | 10 | 20 | 60.0% | 80.0% | 73.3% | 70.0% | 90.0% | 83.3% | 70.0% | 90.0% | 83.3% |
STE20 | 10 | 20 | 70.0% | 75.0% | 73.3% | 80.0% | 90.0% | 86.7% | 80.0% | 90.0% | 86.7% |
Phosphorylated Threonine (pThr) | |||||||||||
All Threonine data | 603 | 1206 | 60.9% | 59.7% | 60.1% | 67.8% | 67.2% | 67.4% | 70.1% | 72.5% | 71.3% |
MAPK | 13 | 26 | 69.2% | 76.9% | 74.3% | 69.2% | 76.9% | 74.3% | 69.2% | 76.9% | 74.3% |
PKA | 10 | 20 | 70.0% | 90.0% | 83.3% | 80.0% | 85.0% | 83.3% | 80.0% | 95.0% | 90.0% |
PKC | 13 | 26 | 61.5% | 76.9% | 71.8% | 69.2% | 88.5% | 82.1% | 69.2% | 88.5% | 82.1% |
STE20 | 10 | 20 | 40.0% | 95.0% | 76.7% | 70.0% | 70.0% | 70.0% | 70.0% | 90.0% | 80.0% |
Phosphorylated Tyrosine (pTyr) | |||||||||||
All tyrosine data | 629 | 1258 | 62.0% | 63.3% | 62.8% | 64.1% | 63.4% | 63.8% | 67.6% | 68.6% | 68.3% |
Abl | 18 | 36 | 50.0% | 88.9% | 75.9% | 66.7% | 80.6% | 75.9% | 66.7% | 80.6% | 75.9% |
EGFR | 10 | 20 | 60.0% | 80.0% | 73.3% | 60.0% | 95.0% | 83.3% | 60.0% | 95.0% | 83.3% |
InsR | 15 | 30 | 73.3% | 83.3% | 80.0% | 80.0% | 80.0% | 80.0% | 80.0% | 90.0% | 86.7% |
Src | 57 | 114 | 77.2% | 75.4% | 76.0% | 79.1% | 83.3% | 81.9% | 79.1% | 84.9% | 82.9% |
Syk | 11 | 22 | 63.6% | 90.9% | 81.8% | 72.7% | 86.4% | 81.8% | 72.7% | 95.5% | 87.9% |