Table 1.
Sensitivity (a), specificity (b) and PPV (c) of the prediction of different data sets by varying the filtering conditions
| Data set | 90% identity |
70% identity |
30% identity |
eggNOG | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All | Dom | GO | COG | All | Dom | GO | COG | All | Dom | GO | COG | All | |
| Arabidopsis (a) | 17% | 3% | 8% | 7% | 31% | 5% | 16% | 13% | 53% | 8% | 25% | 21% | 32% |
| Yeast (a) | 13% | 0% | 4% | 6% | 17% | 0% | 5% | 6% | 30% | 1% | 10% | 14% | 33% |
| Human (a) | 11% | 1% | 5% | 4% | 23% | 2% | 10% | 8% | 42% | 4% | 17% | 15% | 28% |
| Mouse (a) | 17% | 1% | 6% | 8% | 36% | 2% | 12% | 14% | 59% | 3% | 18% | 20% | 27% |
| Drosophila (a) | 4% | 0% | 1% | 0% | 5% | 0% | 1% | 1% | 10% | 1% | 2% | 2% | 8% |
| Worm (a) | 1% | 0% | 0% | 0% | 4% | 1% | 2% | 1% | 12% | 2% | 6% | 4% | 11% |
| Negatome (b) | 92% | 98% | 95% | 97% | 88% | 97% | 91% | 96% | 72% | 92% | 78% | 97% | 77% |
| Arabidopsis (c)(d) | 1.27% | 4.92% | 2.33% | 1.67% | 0.56% | 4% | 1.23% | 0.63% | 0.07% | 0.56% | 0.17% | 0.06% | 0.03% |
The percentage indicates sensitivity (a), specificity (b) or PPV (c). (d) Main screen data set from the Arabidopsis interactome map for 8 596 Arabidopsis proteins, with a precision of 80% and a sensitivity of 16% (38). All, all predictions without applying any restriction; Dom, predictions filtered by known interacting domains reported in 3DID or iPfam; GO, predictions filtered by GO term similarity (biological process or cellular compartment); COG, predictions filtered by known interacting proteins in the same clusters of orthologous groups. Clusters of orthologous genes were as defined in the eggNOG database excluding non-supervised clusters.