From: Improving protein function prediction using domain and protein complexes in PPI networks
Data set | Methods | MF | CC | BP | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
 |  | #GO | PPV | TPR | Fmeasure | MCC | #GO | PPV | TPR | Fmeasure | MCC | #GO | PPV | TPR | Fmeasure | MCC |
MIPS | DSCP | 83 | 0.49 | 0.41 | 0.44 | 0.44 | 113 | 0.43 | 0.40 | 0.41 | 0.40 | 249 | 0.37 | 0.37 | 0.37 | 0.36 |
DCS | 83 | 0.42 | 0.34 | 0.38 | 0.37 | 113 | 0.30 | 0.28 | 0.29 | 0.28 | 249 | 0.30 | 0.31 | 0.30 | 0.30 | |
Zhang-DC | 83 | 0.24 | 0.19 | 0.21 | 0.20 | 113 | 0.21 | 0.21 | 0.21 | 0.20 | 249 | 0.23 | 0.24 | 0.24 | 0.23 | |
MRF | 83 | 0.36 | 0.22 | 0.27 | 0.28 | 113 | 0.19 | 0.11 | 0.14 | 0.14 | 249 | 0.18 | 0.13 | 0.15 | 0.15 | |
RLC | 83 | 0.19 | 0.32 | 0.24 | 0.23 | 113 | 0.20 | 0.37 | 0.26 | 0.25 | 249 | 0.16 | 0.37 | 0.22 | 0.22 | |
DIP | DSCP | 95 | 0.47 | 0.40 | 0.43 | 0.43 | 124 | 0.45 | 0.43 | 0.44 | 0.43 | 267 | 0.38 | 0.37 | 0.38 | 0.37 |
DCS | 95 | 0.45 | 0.38 | 0.41 | 0.41 | 124 | 0.37 | 0.35 | 0.36 | 0.35 | 267 | 0.34 | 0.34 | 0.34 | 0.33 | |
Zhang-DC | 95 | 0.28 | 0.25 | 0.26 | 0.26 | 124 | 0.28 | 0.31 | 0.29 | 0.28 | 267 | 0.25 | 0.27 | 0.26 | 0.25 | |
MRF | 95 | 0.33 | 0.24 | 0.27 | 0.27 | 124 | 0.19 | 0.12 | 0.14 | 0.14 | 267 | 0.20 | 0.13 | 0.15 | 0.15 | |
RLC | 95 | 0.18 | 0.34 | 0.24 | 0.22 | 124 | 0.19 | 0.46 | 0.27 | 0.27 | 267 | 0.14 | 0.41 | 0.21 | 0.22 | |
Biogrid-phy | DSCP | 103 | 0.48 | 0.42 | 0.45 | 0.44 | 130 | 0.46 | 0.46 | 0.46 | 0.45 | 299 | 0.40 | 0.39 | 0.40 | 0.39 |
DCS | 103 | 0.45 | 0.41 | 0.43 | 0.42 | 130 | 0.40 | 0.44 | 0.42 | 0.41 | 299 | 0.36 | 0.37 | 0.37 | 0.36 | |
Zhang-DC | 103 | 0.32 | 0.29 | 0.31 | 0.30 | 130 | 0.35 | 0.42 | 0.38 | 0.37 | 299 | 0.30 | 0.32 | 0.31 | 0.30 | |
MRF | 103 | 0.48 | 0.26 | 0.34 | 0.35 | 130 | 0.21 | 0.14 | 0.17 | 0.16 | 299 | 0.38 | 0.13 | 0.19 | 0.22 | |
RLC | 103 | 0.15 | 0.29 | 0.20 | 0.17 | 130 | 0.16 | 0.50 | 0.25 | 0.25 | 299 | 0.25 | 0.34 | 0.29 | 0.25 | |
Biogrid-cpl | DSCP | 105 | 0.48 | 0.42 | 0.44 | 0.43 | 130 | 0.45 | 0.46 | 0.45 | 0.45 | 303 | 0.40 | 0.40 | 0.40 | 0.39 |
DCS | 105 | 0.43 | 0.40 | 0.41 | 0.41 | 130 | 0.39 | 0.42 | 0.41 | 0.40 | 303 | 0.36 | 0.39 | 0.37 | 0.36 | |
Zhang-DC | 105 | 0.30 | 0.26 | 0.28 | 0.27 | 130 | 0.32 | 0.38 | 0.35 | 0.34 | 303 | 0.26 | 0.31 | 0.28 | 0.27 | |
MRF | 105 | 0.74 | 0.25 | 0.38 | 0.43 | 130 | 0.52 | 0.13 | 0.21 | 0.26 | 303 | 0.45 | 0.13 | 0.20 | 0.24 | |
 | RLC | 105 | 0.32 | 0.26 | 0.29 | 0.23 | 130 | 0.35 | 0.35 | 0.35 | 0.29 | 303 | 0.22 | 0.35 | 0.27 | 0.25 |