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%)
|
-
↵a Using inflation index I = 2.5 (see text).
-
↵b 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).
-
↵c Percent of sequences grouped by OrthoMCL (left) or EGO (right).
-
↵d Percent of sequences grouped by both OrthoMCL and EGO.
-
↵e Coherent (but not identical) groups extended by EGO (EGO ⊃ OrthoMCL).
-
↵f Coherent (but not identical) groups extended by OrthoMCL (OrthoMCL ⊃ EGO).
-
↵g Percent of OrthoMCL groups (left); percent of EGO groups (right).
-
↵h OrthoMCL groups entirely contained within EGO groups (left); EGO groups entirely contained within OrthoMCL groups (right).
-
↵i Percent of OrthoMCL groups (regardless of species distribution).
-
↵j Percent of EGO groups (regardless of species distribution).
-
↵k Percent of all sequences grouped by OrthoMCL (regardless of species distribution).
-
↵l Percent of all sequences grouped by EGO (regardless of species distribution).
