Table 3 Changes in support after updates to orthology-prediction methods
ClassType of supportNo. of genesPercent of class (%)Representation with respect to proportion in OL1 (significance)Total genesin classPercent of OL1 (%)
Stayed the sameUnique116421.2Unchanged (P = 0.4340)548772.5
Two58910.7Underrepresented (P < 0.001)
Three88216.1Underrepresented (P < 0.001)
Four285252.0Overrepresented (P < 0.001)
Lost supportUnique to lost26020.2Unchanged (P = 0.2205)128517.0
Two to unique18414.3Overrepresented (P = 0.0034)
Two to lost272.1
Three to two25319.7Unchanged (P = 0.2034)
Three to unique262.0
Three to lost00.0
Four to three49238.3Underrepresented (P = 0.0406)
Four to two383.0
Four to unique50.4
Four to lost00.0
Gained supportUnique to two20025.1Overrepresented (P < 0.001)79710.5
Unique to three232.9
Unique to four30.4
Two to three17622.1Overrepresented (P < 0.001)
Two to four334.1
Three to four36245.4Overrepresented (P < 0.001)
  • All statistics in this table are calculated by a two-tailed, chi-square with Yates correction. The majority of genes (72.5%) from OL1 retained the same level of support, but significantly more lost support rather than gained it after updates (P > 0.001). To ask if there was a trend toward stability based on degree of support, we looked at whether genes supported by more programs in OL1 were overrepresented in the class that retained—or gained—support, or whether they were underrepresented in the class of genes that lost support. Conversely, we looked for whether genes supported by fewer programs were overrepresented in the class of genes that lost support. We did not find strong evidence for such a trend. The proportion of uniques within the class that retained the same level of support, or lost it, was not significantly different from the proportion of uniques in OL1. Moreover, uniques were overrepresented in the class that gained support. Therefore, being a unique is not a predictor for remaining unique or losing support. We also noticed that genes supported by two programs were as likely to lose support as they were to gain it (overrepresented in both classes), while genes supported by three or four programs are less likely to lose support upon updates.