Inferring gene function from evolutionary change in signatures of translation efficiency

The "numOrgs" column shows a number of organisms positive for the given trait, and the total number of organisms where that trait is defined. For instance, traits named "Mammalian pathogen: (tissue or organ)" are positive for pathogens infecting that organ, negative for all other mammalian pathogens, and undefined for the rest of examined Bacteria and Archaea. In some cases (e.g. halophiles), many microbes have undefined values due to missing annotations.

In every COG, column "a" is the number of HE genes in microbes positive for the given trait, "b" is the count of non-HE genes in the same microbes, "c" is HE genes in microbes where the trait is negative and "d" is the count of non-HE genes in the negative organisms. "Enrich" is the enrichment = a/(a+b) / ( c/(c+d) ). (Table B) Same as table A, but with the threshold for the RF test for counfounders slightly relaxed to P<0.05, yielding 167 additional COG-phenotype links (total: 367).

(Table C) A set of 2386 inferred COG-phenotype links with broader coverage due to relaxed criteria for magnitude of enrichment (1.5x or 0.66x, instead of 2x or 0.5x); the criteria for significance of the enrichment remained the same (P<0.01 in Fisher's exact test). Additionally, the COG-phenotype links in this table did not have to pass the RF randomization test for confounders (meaning there is no control for phylogeny, genome size/GC content, or the inter-correlation of phenotypes).