From: Positive-unlabelled learning of glycosylation sites in the human proteome
Type | Algorithm | 2007 | 2010 | 2013 | ||||||
---|---|---|---|---|---|---|---|---|---|---|
F1 | ACC | AUC | F1 | ACC | AUC | F1 | ACC | AUC | ||
C | PA2DE (V2.0) | 0.917 ± 0.049 | 0.909 ± 0.041 | 0.975 ± 0.061 | 0.917 ± 0.147 | 0.917 ± 0.087 | 0.948 ± 0.074 | 0.917 ± 0.034 | 0.923 ± 0.073 | 0.941 ± 0.037 |
PA2DE | 0.910 ± 0.051 | 0.904 ± 0.055 | 0.966 ± 0.039 | 0.898 ± 0.049 | 0.890 ± 0.054 | 0.925 ± 0.055 | 0.915 ± 0.044 | 0.910 ± 0.049 | 0.937 ± 0.046 | |
PAODE | 0.843 ± 0.082 | 0.843 ± 0.077 | 0.912 ± 0.071 | 0.826 ± 0.111 | 0.837 ± 0.086 | 0.902 ± 0.083 | 0.870 ± 0.083 | 0.870 ± 0.074 | 0.933 ± 0.060 | |
PNB | 0.889 ± 0.047 | 0.872 ± 0.060 | 0.943 ± 0.048 | 0.906 ± 0.047 | 0.895 ± 0.057 | 0.923 ± 0.047 | 0.908 ± 0.046 | 0.899 ± 0.056 | 0.936 ± 0.043 | |
PTAN | 0.861 ± 0.056 | 0.841 ± 0.070 | 0.932 ± 0.049 | 0.887 ± 0.053 | 0.875 ± 0.064 | 0.923 ± 0.053 | 0.918 ± 0.046 | 0.912 ± 0.052 | 0.951 ± 0.039 | |
PFBC | 0.869 ± 0.049 | 0.846 ± 0.066 | 0.947 ± 0.042 | 0.882 ± 0.045 | 0.866 ± 0.058 | 0.935 ± 0.044 | 0.893 ± 0.054 | 0.879 ± 0.068 | 0.940 ± 0.046 | |
RF[a] | 0.847 ± 0.070 | 0.835 ± 0.075 | 0.922 ± 0.064 | 0.864 ± 0.058 | 0.856 ± 0.059 | 0.922 ± 0.056 | 0.883 ± 0.057 | 0.875 ± 0.062 | 0.941 ± 0.051 | |
SVM | 0.810 ± 0.095 | 0.814 ± 0.080 | 0.814 ± 0.080 | 0.851 ± 0.083 | 0.853 ± 0.073 | 0.853 ± 0.073 | 0.847 ± 0.085 | 0.855 ± 0.068 | 0.855 ± 0.068 | |
O-SVM[b] | 0.365 ± 0.152 | 0.612 ± 0.065 | 0.612 ± 0.065 | 0.400 ± 0.151 | 0.613 ± 0.066 | 0.613 ± 0.066 | 0.366 ± 0.136 | 0.606 ± 0.055 | 0.606 ± 0.055 | |
O-Classifier[c] | 0.680 ± 0.142 | 0.760 ± 0.081 | 0.760 ± 0.081 | 0.662 ± 0.139 | 0.740 ± 0.082 | 0.740 ± 0.082 | 0.726 ± 0.122 | 0.785 ± 0.076 | 0.785 ± 0.076 | |
N | PA2DE (V2.0) | 0.933 ± 0.041 | 0.928 ± 0.051 | 0.929 ± 0.012 | 0.989 ± 0.011 | 0.985 ± 0.003 | 0.998 ± 0.013 | 0.990 ± 0.012 | 0.985 ± 0.003 | 0.998 ± 0.011 |
PA2DE | 0.916 ± 0.007 | 0.910 ± 0.008 | 0.914 ± 0.008 | 0.987 ± 0.003 | 0.983 ± 0.004 | 0.998 ± 0.002 | 0.988 ± 0.003 | 0.984 ± 0.004 | 0.998 ± 0.001 | |
PAODE | 0.916 ± 0.009 | 0.910 ± 0.009 | 0.943 ± 0.026 | 0.940 ± 0.051 | 0.920 ± 0.049 | 0.928 ± 0.018 | 0.957 ± 0.004 | 0.938 ± 0.006 | 0.928 ± 0.015 | |
PNB | 0.916 ± 0.009 | 0.910 ± 0.009 | 0.943 ± 0.026 | 0.948 ± 0.005 | 0.928 ± 0.007 | 0.923 ± 0.009 | 0.957 ± 0.004 | 0.938 ± 0.006 | 0.925 ± 0.009 | |
PTAN | 0.985 ± 0.004 | 0.985 ± 0.004 | 0.996 ± 0.002 | 0.929 ± 0.010 | 0.899 ± 0.015 | 0.915 ± 0.010 | 0.939 ± 0.010 | 0.909 ± 0.015 | 0.920 ± 0.009 | |
PFBC | 0.916 ± 0.008 | 0.910 ± 0.009 | 0.945 ± 0.029 | 0.949 ± 0.005 | 0.929 ± 0.007 | 0.937 ± 0.022 | 0.957 ± 0.004 | 0.938 ± 0.006 | 0.937 ± 0.021 | |
RF[a] | 0.980 ± 0.005 | 0.980 ± 0.005 | 0.994 ± 0.003 | 0.984 ± 0.004 | 0.978 ± 0.005 | 0.997 ± 0.002 | 0.985 ± 0.003 | 0.979 ± 0.004 | 0.997 ± 0.002 | |
SVM | 0.916 ± 0.007 | 0.910 ± 0.008 | 0.910 ± 0.008 | 0.948 ± 0.005 | 0.928 ± 0.007 | 0.912 ± 0.009 | 0.957 ± 0.004 | 0.938 ± 0.006 | 0.916 ± 0.009 | |
O-SVM[b] | 0.551 ± 0.125 | 0.695 ± 0.695 | 0.695 ± 0.061 | 0.553 ± 0.108 | 0.585 ± 0.069 | 0.695 ± 0.051 | 0.567 ± 0.097 | 0.570 ± 0.066 | 0.701 ± 0.046 | |
O-Classifier[c] | 0.868 ± 0.052 | 0.850 ± 0.045 | 0.894 ± 0.045 | 0.871 ± 0.037 | 0.855 ± 0.043 | 0.897 ± 0.036 | 0.923 ± 0.042 | 0.896 ± 0.051 | 0.904 ± 0.038 | |
O | PA2DE (V2.0) | 0.979 ± 0.007 | 0.979 ± 0.011 | 0.995 ± 0.007 | 0.986 ± 0.007 | 0.986 ± 0.010 | 0.997 ± 0.006 | 0.982 ± 0.013 | 0.982 ± 0.007 | 0.996 ± 0.012 |
PA2DE | 0.977 ± 0.011 | 0.978 ± 0.011 | 0.996 ± 0.012 | 0.983 ± 0.008 | 0.983 ± 0.008 | 0.997 ± 0.002 | 0.977 ± 0.013 | 0.977 ± 0.013 | 0.996 ± 0.005 | |
PAODE | 0.968 ± 0.012 | 0.968 ± 0.013 | 0.994 ± 0.004 | 0.980 ± 0.010 | 0.980 ± 0.009 | 0.998 ± 0.002 | 0.967 ± 0.011 | 0.968 ± 0.010 | 0.995 ± 0.005 | |
PNB | 0.984 ± 0.007 | 0.984 ± 0.007 | 0.997 ± 0.002 | 0.967 ± 0.010 | 0.966 ± 0.011 | 0.998 ± 0.001 | 0.980 ± 0.009 | 0.980 ± 0.008 | 0.997 ± 0.002 | |
PTAN | 0.938 ± 0.016 | 0.936 ± 0.017 | 0.987 ± 0.007 | 0.942 ± 0.013 | 0.940 ± 0.014 | 0.988 ± 0.006 | 0.935 ± 0.014 | 0.932 ± 0.015 | 0.987 ± 0.006 | |
PFBC | 0.967 ± 0.012 | 0.966 ± 0.013 | 0.998 ± 0.002 | 0.965 ± 0.011 | 0.965 ± 0.011 | 0.995 ± 0.003 | 0.963 ± 0.010 | 0.962 ± 0.010 | 0.993 ± 0.004 | |
RF[a] | 0.979 ± 0.016 | 0.979 ± 0.016 | 0.994 ± 0.006 | 0.980 ± 0.016 | 0.981 ± 0.015 | 0.996 ± 0.004 | 0.967 ± 0.011 | 0.968 ± 0.010 | 0.995 ± 0.005 | |
SVM | 0.977 ± 0.011 | 0.978 ± 0.011 | 0.996 ± 0.012 | 0.974 ± 0.014 | 0.974 ± 0.013 | 0.996 ± 0.005 | 0.981 ± 0.014 | 0.981 ± 0.013 | 0.994 ± 0.005 | |
O-SVM[b] | 0.582 ± 0.053 | 0.691 ± 0.026 | 0.691 ± 0.026 | 0.575 ± 0.575 | 0.681 ± 0.028 | 0.681 ± 0.028 | 0.578 ± 0.045 | 0.666 ± 0.027 | 0.666 ± 0.027 | |
O-Classifier[c] | 0.695 ± 0.039 | 0.593 ± 0.080 | 0.593 ± 0.080 | 0.665 ± 0.026 | 0.535 ± 0.059 | 0.535 ± 0.059 | 0.702 ± 0.026 | 0.621 ± 0.059 | 0.621 ± 0.059 |