Inferring gene function from evolutionary change in signatures of translation efficiency

<strong>Krisko, Copic, Gabaldon, Lehner and Supek. Genome Biol 2014.</strong> doi:10.1186/gb-2014-15-3-r44<br><strong>"Inferring gene function from evolutionary change in signatures of translation efficiency"</strong> Additional file 18. All COG gene families found to be significantly enriched/depleted for<br>highly expressed (HE) genes across 911 microbial genomes in any of the 24 examined<br>phenotypes or environments. The HE genes were determined by quantifying the use of<br>optimal codons, which was compared against the composition of intergenic DNA<br>using a randomization test. <strong>(Table A)</strong> All 200 shown expression-phenotype links have (i) Fisher's exact test<br>for enrichment P&lt;0.01, (ii) magnitude of enrichment &gt;2x or &lt;0.5x, and<br>(iii) Random Forest (RF) randomization test for confounding<br>phenotypes/environments/phylogeny P&lt;0.01. A total of 187 unique COGs are<br>represented in the list. The "numOrgs" column shows a number of organisms positive for the given trait,<br>and the total number of organisms where that trait is defined. For instance,<br>traits named "Mammalian pathogen: (tissue or organ)" are positive for pathogens<br>infecting that organ, negative for all other mammalian pathogens,<br>and undefined for the rest of examined Bacteria and Archaea. In some cases<br>(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,<br>"b" is the count of non-HE genes in the same microbes, "c" is HE genes in microbes where<br>the trait is negative and "d" is the count of non-HE genes in the negative organisms.<br>"Enrich" is the enrichment = a/(a+b) / ( c/(c+d) ). <strong>(Table B)</strong> Same as table A, but with the threshold for the RF test for counfounders<br>slightly relaxed to P&lt;0.05, yielding 167 additional COG-phenotype links (total: 367). <strong>(Table C)</strong> A set of 2386 inferred COG-phenotype links with broader coverage due to relaxed<br>criteria for magnitude of enrichment (1.5x or 0.66x, instead of 2x or 0.5x); the criteria<br>for significance of the enrichment remained the same (P&lt;0.01 in Fisher's exact test).<br>Additionally, the COG-phenotype links in this table did not have to pass the<br>RF randomization test for confounders (meaning there is no control for phylogeny,<br>genome size/GC content, or the inter-correlation of phenotypes).