From: SAlign–a structure aware method for global PPI network alignment
Pairs | Evaluation criteria | SA | \(\hbox {SA}^{\mathrm{mc}}\) | HA | MA | IBN | NET | M++ | PRO |
---|---|---|---|---|---|---|---|---|---|
Results on HINT datasets (a) | |||||||||
Mouse human | AFS\(_{MF}\) | 0.58 | 0.55 | 0.48 | 0.42 | 0.35 | 0.33 | 0.36 | 0.58 |
AFS\(_{BP}\) | 0.43 | 0.41 | 0.34 | 0.30 | 0.26 | 0.24 | 0.26 | 0.45 | |
Nodes\(_{MF}\) | 82 | 82 | 78 | 74 | 72 | 73 | 76 | 82 | |
Nodes\(_{BP}\) | 85 | 86 | 84 | 81 | 83 | 82 | 82 | 84 | |
Mouse yeast | AFS\(_{MF}\) | 0.40* | 0.39 | 0.36 | 0.31 | 0.29 | 0.31 | 0.29 | 0.36 |
AFS\(_{BP}\) | 0.27* | 0.26 | 0.25 | 0.23 | 0.21 | 0.22 | 0.21 | 0.25 | |
Nodes\(_{MF}\) | 72 | 73 | 71 | 71 | 63 | 64 | 67 | 53 | |
Nodes\(_{BP}\) | 92 | 91 | 90 | 88 | 76 | 83 | 83 | 69 | |
Human yeast | AFS\(_{MF}\) | 0.48* | 0.46 | 0.46 | 0.26 | 0.30 | 0.26 | 0.26 | 0.42 |
AFS\(_{BP}\) | 0.35* | 0.33 | 0.34 | 0.22 | 0.24 | 0.22 | 0.22 | 0.32 | |
Nodes\(_{MF}\) | 64 | 63 | 63 | 60 | 58 | 60 | 59 | 57 | |
Nodes\(_{BP}\) | 76 | 76 | 76 | 72 | 70 | 72 | 70 | 68 | |
Avg. | AFS\(_{MF}\) | 0.49 | 0.47 | 0.43 | 0.33 | 0.31 | 0.30 | 0.31 | 0.45 |
AFS\(_{BP}\) | 0.35 | 0.33 | 0.31 | 0.25 | 0.24 | 0.23 | 0.24 | 0.34 | |
Nodes\(_{MF}\) | 73 | 73 | 71 | 68 | 64 | 66 | 67 | 64 | |
Nodes\(_{BP}\) | 84 | 84 | 83 | 80 | 76 | 79 | 78 | 74 | |
Results on BioGRID datasets (b) | |||||||||
Mouse human | AFS\(_{MF}\) | 0.64 | 0.63 | 0.57 | 0.46 | 0.35 | 0.33 | 0.36 | 0.63 |
AFS\(_{BP}\) | 0.48 | 0.47 | 0.43 | 0.35 | 0.27 | 0.26 | 0.28 | 0.48 | |
Nodes\(_{MF}\) | 89 | 89 | 88 | 85 | 80 | 83 | 86 | 83 | |
Nodes\(_{BP}\) | 96 | 96 | 95 | 93 | 90 | 93 | 96 | 93 | |
Mouse yeast | AFS\(_{MF}\) | 0.47 | 0.46 | 0.44 | 0.37 | 0.28 | 0.27 | 0.33 | 0.47 |
AFS\(_{BP}\) | 0.32 | 0.32 | 0.29 | 0.27 | 0.22 | 0.22 | 0.22 | 0.32 | |
Nodes\(_{MF}\) | 82 | 82 | 80 | 80 | 76 | 77 | 80 | 58 | |
Nodes\(_{BP}\) | 96 | 96 | 94 | 97 | 88 | 92 | 97 | 67 | |
Human yeast | AFS\(_{MF}\) | 0.53* | 0.52 | 0.48 | 0.42 | 0.34 | 0.28 | 0.29 | 0.49 |
AFS\(_{BP}\) | 0.39* | 0.38 | 0.35 | 0.33 | 0.27 | 0.23 | 0.24 | 0.38 | |
Nodes\(_{MF}\) | 74 | 74 | 73 | 74 | 63 | 72 | 70 | 67 | |
Nodes\(_{BP}\) | 91 | 91 | 91 | 91 | 77 | 91 | 90 | 82 | |
Avg. | AFS\(_{MF}\) | 0.55 | 0.54 | 0.50 | 0.42 | 0.32 | 0.29 | 0.33 | 0.53 |
AFS\(_{BP}\) | 0.40 | 0.39 | 0.36 | 0.32 | 0.25 | 0.24 | 0.25 | 0.39 | |
Nodes\(_{MF}\) | 82 | 82 | 80 | 80 | 73 | 77 | 79 | 69 | |
Nodes\(_{BP}\) | 94 | 94 | 93 | 94 | 85 | 92 | 94 | 79 |