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Table 2 Associations between COGs and descriptive variables.

From: Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes

COG Number of gene analyzed Bonferroni-corrected P value for one-sided U-test testing for associations between genes in a given COG and(1)
   > length > nt diversity > Number of Informative sites > Codon bias(2) < Codon bias(2)
Energy production and conversion 100 < 0.002 ND NS 0.007 ND
Cell cycle control, mitosis and meiosis 20 NS ND ND NS ND
Amino acid transport and metabolism 181 < 0.002 NS < 0.002 NS ND
Nucleotide transport and metabolism 63 NS ND NS NS ND
Carbohydrate transport and metabolism 186 < 0.002 ND NS NS ND
Coenzyme transport and metabolism 87 NS < 0.001 0.004 ND 0.047
Lipid transport and metabolism 51 NS NS NS NS ND
Translation 91 NS ND ND < 0.001 ND
Transcription 187 ND ND ND ND < 0.002
Replication, recombination and repair 92 < 0.002 < 0.001 < 0.002 ND NS
Cell wall/membrane biogenesis 76 < 0.002 < 0.001 < 0.002 NS ND
Cell motility 40 NS ND NS ND NS
Posttranslational modification, protein turnover, chaperones 52 ND ND ND 0.021 ND
Inorganic ion transport and metabolism 104 NS ND NS ND NS
Secondary metabolites biosynthesis, transport and catabolism 31 ND NS NS ND NS
General function prediction only 254 NS NS 0.008 ND NS
Function unknown 161 ND NS ND ND NS
Signal transduction mechanisms 104 NS ND NS ND < 0.002
Intracellular trafficking and secretion 37 NS ND ND NS ND
Defense mechanisms 51 < 0.002 NS 0.020 ND NS
Not in COGs 511 ND ND ND ND NS
  1. (1) ">" or "<" indicates the direction of the one-sided tests (i.e. column "> Codon bias" shows Bonferroni-corrected p-values for associations between genes in a given COG and higher codon bias (as compared to the genes in other COGs), while the column "< Codon bias" test shows Bonferroni-corrected p-values for genes in COGs with lower codon bias as compared to genes in other COGs; "ND" = Not determined (tests were not performed for COGs that showed values that were not consistent with the tested alternative hypothesis, e.g., if the average gene length for genes in a given COG was below average than we did not test for an association of this COG with increased gene length); "NS". Not significant.
  2. (2)Tests for codon bias were performed using Nc values; a lower Nc indicates increased codon bias.