Table 3. Genes, gene ontologies and expression pathways exhibiting the most significant enrichments or depletions of protein-altering B-class variants separating nose and infection site bacteria.
Gene group | No. protein-altering B-class variants |
Cumulative lengthof genes (kb) | Enrichment | Significance (-log10 p value) | |||
---|---|---|---|---|---|---|---|
Locus | |||||||
agrA | 5 | 0.7 | 58.27 | 7.53 | |||
clfB | 5 | 2.6 | 15.87 | 4.70 | |||
Total | 289 | 2363.8 | |||||
BioCyc Gene Ontology (Caspi et al., 2016) | |||||||
Cell wall | 18 | 30.9 | 5.02 | 7.03 | |||
Cell adhesion | 13 | 17.2 | 6.44 | 6.47 | |||
Pathogenesis | 31 | 112.5 | 2.41 | 4.44 | |||
Total | 288 | 2359.3 | |||||
SAMMD Expression Pathway | Down-regulated | Up-regulated | Down-regulated | Up-regulated | Down-regulated | Up-regulated | |
Ovispirin-1 (Pietiäinen et al., 2009) | 40 | 7 | 121.2 | 142.9 | 2.65 | 0.39 | 7.80 |
Temporin L (Pietiäinen et al., 2009) | 42 | 14 | 125.1 | 156.1 | 2.78 | 0.74 | 6.86 |
rsp (Lei et al., 2011) | 27 | 1 | 61.1 | 13.7 | 3.61 | 0.60 | 6.35 |
agrA (RN27) (Dunman et al., 2001) | 9 | 30 | 41.0 | 85.0 | 1.83 | 2.94 | 5.57 |
VISA-vs-VSSA (Mu50 vs N315) (Cui et al., 2005) | 0 | 17 | 0 | 34.4 | 0 | 3.95 | 5.27 |
VISA-vs-VSSA (Mu50 vs Mu50-P) (Cui et al., 2005) | 0 | 17 | 0 | 36.7 | 0 | 3.70 | 4.90 |
VISA-vs-VSSA (isolate pair 2) (Howden et al., 2008) | 14 | 3 | 26.9 | 59.7 | 4.06 | 0.39 | 4.71 |
sarA (RN27) (Dunman et al., 2001) | 6 | 23 | 49.9 | 57.7 | 0.97 | 3.22 | 4.59 |
agrA (UAMS-1 OD 1.0) (Cassat et al., 2006) | 0 | 5 | 0 | 2.7 | 0 | 14.57 | 4.52 |
Pine-Oil Disinfectant-Reduced-Susceptibility (Lamichhane-Khadka et al., 2008) | 17 | 5 | 36.4 | 23.6 | 3.76 | 1.70 | 4.44 |
Total | 275 | 2093.5 |