Figure 3. All genes contributing to the pathways and ontologies most significantly enriched for protein-altering substitutions between nose-colonizing and infection-causing bacteria.

The pathogenesis ontology, in which significant enrichments were observed in infection-causing but not nose-colonizing bacteria, is shown for comparison. Every gene with at least one substitution between nose-colonizing and infection-causing bacteria and which was up- (red) or down- regulated (blue) in one of the pathways or a member of one of the ontologies (blue) is shown. To the left, the number of altering (yellow/orange) and truncating (pink/red) B-class variants is shown, broken down by the population in which the mutant allele was found: nose (B_C; yellow/pink) or infection site (B_D; orange/red).

Figure 3—figure supplement 1. Genes enriched for substitutions between nose-colonizing and infection-causing bacteria within patients are not the most rapidly evolving at the species level.

An estimate of the d_N/d_S ratio between unrelated bacteria is shown for each gene, color-coded by the number of protein-altering substitutions between nose-colonizing and infection-causing bacteria within patients. There was a negative Spearman rank correlation between d_N/d_S ratio and substitutions within patients (ρ = –0.04, p=0.02).

Figure 3—figure supplement 2. Gene set enrichment analysis is robust to species-level differences in d_N/d_S between genes.

For every locus, expression pathway and gene ontology, we estimated d_N/d_S between unrelated S. aureus. There was no relationship between d_N/d_S and enrichment of protein-altering substitutions between nose-colonizing and infection-causing bacteria in (A) loci, (B) ontologies nor (C) pathways (non-significant correlations, p>0.05). When we incorporated variability in d_N/d_S between genes in the gene set enrichment analyses, the results were robust for (D) loci, (E) ontologies and (F) pathways, showing only small differences in significance (-log₁₀ p-value) between the analyses that correct for locus length only (horizontal axes) and those that correct for locus length and d_N/d_S (vertical axes).