Skip to main content

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
   Os01g66030.1 OsMADS2         
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         
At5g15800.1 SEP1           
At4g18960.1 AG Os01g10504.1 OsMADS3 1/2 16326928 0/3 0 1/1 2 2 1
   Os05g11414.3 OsMADS58         
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           
At1g55580.1 LAS Os06g40780.1 MOC1 1/1 12687001; 12730136 1/2 1/1 1/1 0 0 0
   Os02g10360.1          
At3g54220.1 SCR Os12g02870.1 OsSCR 1/2 12974810 1/2 1/1 1/2 0 1 0
   Os11g03110.1          
At4g37650.1 SHR Os03g31880.1 OsSHR 1/2 12974810 1/2 1/1 1/1 0 1 1
   Os07g39820.1          
At3g11260.1 WOX5 Os01g63510.1 QHB 2/1 12904206; 14711878 2/1 1/1 1/1 0 1 1
At5g05770.1 WOX7           
At4g16280.3 FCA Os09g03610.2   1/1 16240176 1/1 1/1 1/1 0 0 0
At4g00650.1 FRI Os03g63440.1   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
   Os03g49400.1          
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          
   Os02g32950.1 RCN2         
   Os12g05590.1 RCN3         
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
  1. TAIR, TIGR id = accession number from TAIR and TIGR; orth = ortholog relations identified in the literature. GP = Greenphyl; BH = BBMH; INP = Inparanoid; true positives = ortholog relation; missing = ortholog missed by GP, BH or INP. PMID = Pubmed id