Table 3 Comparison between protein complexes defined by small-scale experiments versus those inferred from high-throughput interaction datasets.
Ground truth definition source | Network dataset | SpeakEasy output type | NMI | Omega | Precision | Recall | F-score | Precision (overlapping) | Recall (overlapping) | F-score (overlapping) |
|---|---|---|---|---|---|---|---|---|---|---|
CYC2008 | Collins et al. | Disjoint | 0.7237 | 0.6382 | 0.9844 | 0.8259 | 0.8982 | NA | NA | NA |
CYC2008 | Collins et al. | Overlapping | 0.7120 | 0.5961 | 0.9845 | 0.8055 | 0.8860 | 0.2151 | 0.1170 | 0.1515 |
CYC2008 | Gavin et al. | Disjoint | 0.4502 | 0.4530 | 0.8915 | 0.5395 | 0.6722 | NA | NA | NA |
CYC2008 | Gavin et al. | Overlapping | 0.4498 | 0.4265 | 0.8837 | 0.5292 | 0.6620 | 0.2105 | 0.0958 | 0.1317 |
MIPS | Collins et al. | Disjoint | 0.6669 | 0.3740 | 0.9208 | 0.8701 | 0.8947 | NA | NA | NA |
MIPS | Collins et al. | Overlapping | 0.6665 | 0.3880 | 0.9118 | 0.8588 | 0.8845 | 0.7821 | 0.1227 | 0.2122 |
MIPS | Gavin et al. | Disjoint | 0.5155 | 0.2001 | 0.8889 | 0.7238 | 0.7979 | NA | NA | NA |
MIPS | Gavin et al. | Overlapping | 0.4929 | 0.2259 | 0.9053 | 0.7127 | 0.7975 | 0.7143 | 0.2092 | 0.3236 |
SGD | Collins et al. | Disjoint | 0.7147 | 0.5652 | 0.9597 | 0.7510 | 0.8426 | NA | NA | NA |
SGD | Collins et al. | Overlapping | 0.7058 | 0.5106 | 0.9733 | 0.7470 | 0.8453 | 0.4766 | 0.2048 | 0.2865 |
SGD | Gavin et al. | Disjoint | 0.5474 | 0.5215 | 0.9907 | 0.6255 | 0.7668 | NA | NA | NA |
SGD | Gavin et al. | Overlapping | 0.5460 | 0.5130 | 0.9722 | 0.6175 | 0.7553 | 0.3659 | 0.0652 | 0.1107 |
