Table 2.
Comparison of Ortholog Groups Identified by OrthoMCL vs. EGO
| Total | OrthoMCLa | EGOb | Grouped by both (∩) | Identical groups | EGO extends OrthoMCLe | OrthoMCL extends EGOf | Coherent groups | |
|---|---|---|---|---|---|---|---|---|
| # Protein sequences | 39,420 | 13,851 (35%) | 5,286 (13%) | 4,959 (36/94%)c | 2,432 (49%)d | 158 (3%)d | 3,004 (61%)d | 4,716 (95%)d |
| Yeast data set | 6,358 | 2,531 (40%) | 923 (15%) | 882 (35/96%) | 452 (51%) | 38 (4%) | 617 (70%) | 827 (94%) |
| Fly data set | 13,288 | 5,409 (41%) | 2,138 (17%) | 2,018 (37/94%) | 987 (49%) | 66 (3%) | 1,174 (58%) | 1,928 (96%) |
| Worm data set | 19,774 | 5,911 (30%) | 2,225 (11%) | 2,059 (35/93%) | 993 (48%) | 54 (3%) | 1,213 (59%) | 1,961 (95%) |
| # Groups | 4,425 | 3,620 | not applicable | 989 (22/27%)g | 70 (2%)i | 2,038 (56%)j | 1,059/3,027h (24/84%)g | |
| Yeast, fly not worm | sequences | 586 (4%)k | 816 (17%)l | 56 (10/7%) | 40 (71%) | 2 (4%) | 9 (16%) | 51 (92%) |
| groups | 215 (5%)i | 440 (12%)j | not applicable | 20 (9/5%) | 1 (0.5%) | 5 (1%) | 21/25 (10/6%) | |
| Yeast, worm not fly | sequences | 470 (3%) | 911 (17%) | 62 (13/7%) | 28 (45%) | 0 (0%) | 30 (48%) | 58 (94%) |
| groups | 155 (4%) | 492 (14%) | not applicable | 14 (9/3%) | 0 (0%) | 19 (4%) | 14/33 (9/7%) | |
| Fly, worm not yeast | sequences | 6,337 (46%) | 3,568 (67%) | 1,614 (25/45%) | 1,161 (72%) | 18 (1%) | 390 (24%) | 1,535 (95%) |
| groups | 2,307 (52%) | 1,874 (52%) | not applicable | 571 (25/30%) | 9 (0.4%) | 208 (11%) | 580/779 (25/42%) | |
| Fly, worm and yeast | sequences | 6,458 (47%) | 2,105 (40%) | 1,868 (29/89%) | 1,203 (64%) | 48 (3%) | 654 (35%) | 1,763 (94%) |
| groups | 1,748 (40%) | 814 (22%) | not applicable | 384 (22/47%) | 16 (1%) | 263 (32%) | 400/647 (23/79%) |
Using inflation index I = 2.5 (see text).
See text for description of pruning method used to identify groups containing sequences from at least two of the three species under consideration (yeast, fly, and worm).
Percent of sequences grouped by OrthoMCL (left) or EGO (right).
Percent of sequences grouped by both OrthoMCL and EGO.
Coherent (but not identical) groups extended by EGO (EGO ⊃ OrthoMCL).
Coherent (but not identical) groups extended by OrthoMCL (OrthoMCL ⊃ EGO).
Percent of OrthoMCL groups (left); percent of EGO groups (right).
OrthoMCL groups entirely contained within EGO groups (left); EGO groups entirely contained within OrthoMCL groups (right).
Percent of OrthoMCL groups (regardless of species distribution).
Percent of EGO groups (regardless of species distribution).
Percent of all sequences grouped by OrthoMCL (regardless of species distribution).
Percent of all sequences grouped by EGO (regardless of species distribution).