Table 2 Overlap with ortholog reference set
From: Benchmarking ortholog identification methods using functional genomics data
| Â | Method | Orthologous pairs | Orthologous pairs divided by average proteome size | False positives |
|---|---|---|---|---|
Hox cluster proteins (Hs, 31 unique proteins; Mm, 35 unique proteins; Hs-Mm, 41 protein pairs) | BBH | 26 | 2.03E-03 | 3 |
| Â | INP | 28 | 1.87E-03 | 3 |
| Â | KOG | 30 | 1.65E-03 | 456 |
| Â | MCL | 26 | 1.65E-03 | 25 |
| Â | PGT | 33 | 2.00E-03 | 350 |
| Â | Z1H | 26 | 1.47E-03 | 19 |
Nuclear receptors (Hs, 22 unique proteins; Ce, 18 unique proteins; Hs-Ce, 29 protein pairs) | BBH | 8 | 1.40E-03 | 2 |
| Â | INP | 13 | 1.77E-03 | 179 |
| Â | KOG | 20 | 1.82E-03 | 2,062 |
| Â | MCL | 13 | 2.04E-03 | 4 |
| Â | PGT | 11 | 1.08E-03 | 180 |
| Â | Z1H | 8 | 1.56E-03 | 8 |
Hemoglobins (Hs, 4 unique proteins; Mm, 9 unique proteins; Hs-Mm, 9 protein pairs) | BBH | 2 | 1.56E-04 | 2 |
| Â | INP | 6 | 4.02E-04 | 8 |
| Â | KOG | 4 | 2.20E-04 | 52 |
| Â | MCL | 4 | 2.54E-04 | 3 |
| Â | PGT | 4 | 2.42E-04 | 23 |
| Â | Z1H | 8 | 4.53E-04 | 37 |
Toll-like receptors (Hs, 10 unique proteins; Ce, 1 unique protein; Hs-Ce, 10 protein pairs) | BBH | 0 | 0 | 0 |
| Â | INP | 0 | 0 | 0 |
| Â | KOG | 10 | 9.12E-04 | 1 |
| Â | MCL | 0 | 0 | 0 |
| Â | PGT | 5 | 4.89E-04 | 86 |
| Â | Z1H | 0 | 0 | 0 |
Sm proteins (Hs, 13 unique proteins; Mm, 17 unique proteins; Hs-Mm, 17 protein pairs) | BBH | 5 | 3.90E-04 | 8 |
| Â | INP | 5 | 3.35E-04 | 8 |
| Â | KOG | 6 | 3.29E-04 | 15 |
| Â | MCL | 4 | 2.54E-04 | 10 |
| Â | PGT | 7 | 4.23E-04 | 18 |
| Â | Z1H | 5 | 2.83E-04 | 4 |
Sm proteins (Hs, 6 unique proteins; Ce, 6 unique proteins; Hs-Ce, 6 protein pairs) | BBH | 6 | 1.05E-03 | 0 |
| Â | INP | 6 | 8.19E-04 | 0 |
| Â | KOG | 4 | 3.65E-04 | 1 |
| Â | MCL | 6 | 9.42E-04 | 2 |
| Â | PGT | 3 | 2.93E-04 | 9 |
| Â | Z1H | 0 | 0 | 0 |