Table 2 True positive ortholog test set and ortholog predictions of GreenPhyl (GP), Inparanoid (INP) and BBMH (BH).
From: Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants
Arabidopsis thaliana | Oryza sativa | Orthologs | True positive | Missing | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
TAIR id | Alias | TIGR id | Alias | n/n | PMID | GP | BH | INP | GP | BH | INP |
At5g20240.1 | PI | Os05g34940.1 | OsMADS4 | 1/2 | 14704206 | 1/2 | 1/1 | 1/2 | 0 | 1 | 0 |
| Â | Â | Os01g66030.1 | OsMADS2 | Â | Â | Â | Â | Â | Â | Â | Â |
At3g54340.1 | AP3/DEF | Os06g49840.1 | SPW1 | 1/1 | 12506001 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At1g24260.1 | SEP3 | Os09g32948.1 | OsMADS8 | 3/2 | 16968881; 17205197; 10821278 | 3/2 | 1/1 | 1/1 | 0 | 5 | 5 |
At3g02310.1 | SEP2 | Os08g41950.2 | OsMADS7 | Â | Â | Â | Â | Â | Â | Â | Â |
At5g15800.1 | SEP1 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At4g18960.1 | AG | Os01g10504.1 | OsMADS3 | 1/2 | 16326928 | 0/3 | 0 | 1/1 | 2 | 2 | 1 |
| Â | Â | Os05g11414.3 | OsMADS58 | Â | Â | Â | Â | Â | Â | Â | Â |
At2g45660.1 | SOC1 | Os03g03070.1 | OsMADS50 | 1/1 | 15144377 | 0/3 | 0 | 0 | 1 | 1 | 1 |
At1g14920.1 | GAI | Os03g49990.1 | SLR1 | 2/1 | 11340177; 11826293 | 3/1 | 1/1 | 1/1 | 0 | 1 | 1 |
At2g01570.1 | RGA1 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At1g55580.1 | LAS | Os06g40780.1 | MOC1 | 1/1 | 12687001; 12730136 | 1/2 | 1/1 | 1/1 | 0 | 0 | 0 |
| Â | Â | Os02g10360.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At3g54220.1 | SCR | Os12g02870.1 | OsSCR | 1/2 | 12974810 | 1/2 | 1/1 | 1/2 | 0 | 1 | 0 |
| Â | Â | Os11g03110.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At4g37650.1 | SHR | Os03g31880.1 | OsSHR | 1/2 | 12974810 | 1/2 | 1/1 | 1/1 | 0 | 1 | 1 |
| Â | Â | Os07g39820.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At3g11260.1 | WOX5 | Os01g63510.1 | QHB | 2/1 | 12904206; 14711878 | 2/1 | 1/1 | 1/1 | 0 | 1 | 1 |
At5g05770.1 | WOX7 | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At4g16280.3 | FCA | Os09g03610.2 | Â | 1/1 | 16240176 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At4g00650.1 | FRI | Os03g63440.1 | Â | 1/1 | 12667866 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At2g44990.1 | MAX3 | Os04g46470.1 | HTD1 | 1/1 | 17092317 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At2g42620.1 | MAX2 | Os06g06050.1 | OsMAX2 | 1/1 | 15659436 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At5g03280.1 | EIN2 | Os07g06130.1 | OsEIN2 | 1/1 | 15047876 | 1/2 | 1/1 | 1/3 | 0 | 0 | 0 |
| Â | Â | Os03g49400.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
At5g47120.1 | Bi1 | Os02g03280.1 | OsBi1 | 1/1 | 10618494 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At2g27550.1 | CEN | Os11g05470.1 | RCN1 | 2/3 | 8974397; 12148532 | 2/4 | 1/1 | 1/2 | 0 | 5 | 4 |
At5g03840.1 | TFL1 | Os04g33570.1 | Â | Â | Â | Â | Â | Â | Â | Â | Â |
| Â | Â | Os02g32950.1 | RCN2 | Â | Â | Â | Â | Â | Â | Â | Â |
| Â | Â | Os12g05590.1 | RCN3 | Â | Â | Â | Â | Â | Â | Â | Â |
At1g22770.1 | GI | Os01g08700.1 | OsGI | 1/1 | 12700762 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |
At5g61380.1 | TOC1 | Os02g40510.1 | PRR1 | 1/1 | 14634161 | 1/1 | 1/1 | 1/1 | 0 | 0 | 0 |