Table 2.
Statistics of metabolism class assignments and phylogenetic profile identity of gene families and singletons.
| KEGG metabolism class | NGF/S | Fpw | Fall | E = Fpw/Fall | Adjusted p-value |
|---|---|---|---|---|---|
| Amino acid metabolism (AAM) | 358 | 0.037 | 0.020 | 1.810 | <0.001 |
| Metabolism of other amino acids (MOAA) | 114 | 0.039 | 0.022 | 1.787 | <0.001 |
| Metabolism of cofactors and vitamins (MCV) | 295 | 0.029 | 0.019 | 1.549 | <0.001 |
| Nucleotide metabolism (NM) | 410 | 0.021 | 0.015 | 1.391 | 0.008 |
| Carbohydrate metabolism (CM) | 742 | 0.018 | 0.016 | 1.130 | 0.048 |
| Energy metabolism (EM) | 261 | 0.019 | 0.016 | 1.217 | 0.088 |
| Metabolism of terpenoids and polyketides (MTP) | 84 | 0.018 | 0.013 | 1.435 | 0.327 |
| Biosynthesis of other secondary metabolites (BSM) | 97 | 0.012 | 0.009 | 1.268 | 0.809 |
| Lipid metabolism (LM) | 271 | 0.014 | 0.014 | 0.981 | 0.809 |
| Glycan biosynthesis and metabolism (GBM)) | 145 | 0.008 | 0.009 | 0.930 | 0.991 |
Table lists for all 10 KEGG metabolism classes (KEGG class “Overview” was not considered) the number of gene families or singleton genes (jointly referred to as gene objects, NGF/S) annotated to them, the fraction of all profile-profile comparisons among all NGF/S gene objects yielding identical profiles within a class (Fpw, Equation 1), the fraction of all profile-profile comparisons of NGF/S gene objects yielding identical profiles within and to gene objects outside a class (Fall, Equation 2), the resulting fold enrichment (E = Fpw/Fall) of identical phylogenetic profiles within a class relative to expectation, and 30 associated Benjamini-Hochberg corrected empirical p-value based on 10,000 random class assignments. Results are based on Network30-based gene family assignments (see Methods). Metabolism classes are sorted in ascending order of p-value. Highlighted bold are the secondary metabolism classes.