Table 2

Putative foreign genes in genome islands
Island hitsc
Methoda Total putative foreignb Expected Observed Observed/Totald
Pmm (Prochlorococcus marinus Med4)e
Codon bias 231 28 60* 0.260
CGS 91 11 23* 0.253
W8 96 12 15 0.156
GC 109 13 13 0.119
Pmi(Prochlorococcus marinus MIT9312)e
Codon bias 272 37 56* 0.206
CGS 118 16 29* 0.246
W8 107 15 16 0.150
GC 119 16 25* 0.21

a All methods used a threshold that excludes 95% of the test-native set.

b Genes identified as foreign by the method in the given genome. Pmm has 209 coding genes in genome islands out of a total of 1713 coding genes, and Pmi has 246 coding genes in genome islands out of a total of 1810 coding genes, per Coleman et al. (2006). c The number of genes identified as foreign by the method that lie within a genome island. The expected number is that which would arise if the genes identified as foreign were distributed randomly throughout the genome. Asterisks indicate statistical significance to the level Pā€‰<ā€‰0.001. Numbers without asterisks are not significant even to Pā€‰<ā€‰0.05. d The fraction of total putative foreign genes identified by the method that lie within genome islands.

Elhai et al.

Elhai et al. BMC Genomics 2012 13:245   doi:10.1186/1471-2164-13-245

Open Data