Table 2 Changes in gene number and content after updates to orthology-prediction methods
Gene numbers (net change)Gene content (actual genes in results)
OriginalUpdatedChange (%)No. lostNo. gainedLost (%)Gained (%)
Ensembl Compara64046801+6.2467864−7.3+13.5
HomoloGene41273776−8.5747396−18.1+9.6
InParanoid55915581−0.2290280−5.2+5.0
OrthoMCL56635699+0.65793−1.0+1.6
Mean−0.5Mean−7.9+7.4
SEM±3.0SEM±3.6±2.6
  • The mean change in total number of worm genes with human orthologs predicted by each individual program was quite low (−0.5 ± 3.0%) after updates, although each program showed distinct patterns of change, with Ensembl Compara adding more genes vs. all the other programs losing genes. However, when considering the change in actual gene content, each program appears to have larger changes than what is apparent by just looking at the net change in numbers.