Table 2.
P-values of significant enrichments among clusters of co-regulated genes
| Cluster | # of genes | Growth rate | Substrate | KEGG category | CAZy category | ||
|---|---|---|---|---|---|---|---|
| 1 | 1157 | NS | NS | Bacterial motility proteins | 8.37 × 10−3 | NS | |
| 2 | 507 | NS | NS | Peptidoglycan biosynthesis | 2.12 × 10−3 | CBM51 | 4.70 × 10−2 |
| Polyketide sugar unit biosynthesis | 4.80 × 10−2 | ||||||
| 3 | 412 | NS | NS | Amino acid related enzymes | 1.06 × 10−2 | NS | |
| Aminoacyl-tRNA biosynthesis | 1.63 × 10−2 | ||||||
| Biotin metabolism | 6.17 × 10−3 | ||||||
| Porphyrin and chlorophyll metabolism | 2.16 × 10−3 | ||||||
| Ribosome | 1.29 × 10−14 | ||||||
| Transfer RNA biogenesis | 1.64 × 10−6 | ||||||
| Translation factors | 3.36 × 10−2 | ||||||
| 4 | 167 | 2.70 × 10−6 | 4.80 × 10−19 | NS | NS | ||
| 5 | 164 | NS | NS | Ribosome | 4.36 × 10−9 | NS | |
| 6 | 140 | NS | NS | NS | NS | ||
| 7 | 92 | 6.39 × 10−04 | 2.11 × 10−48 | Chaperones and folding catalysts | 1.64 × 10−2 | NS | |
| Prokaryotic defense system | 3.51 × 10−3 | ||||||
| 8 | 81 | NS | NS | Phenylalanine, tyrosine and tryptophan biosynthesis | 2.56 × 10−2 | GT4 | 1.72 × 10−3 |
| 9 | 78 | 2.83 × 10−27 | 3.48 × 10−16 | ABC transporters | 2.24 × 10−3 | NS | |
| Chloroalkane and chloroalkene degradation | 2.35 × 10−8 | ||||||
| Cysteine and methionine metabolism | 2.56 × 10−7 | ||||||
| Nitrogen metabolism | 2.48 × 10−6 | ||||||
| Quorum sensing | 9.65 × 10−3 | ||||||
| Selenocompound metabolism | 2.75 × 10−5 | ||||||
| Sulfur metabolism | 1.42 × 10−12 | ||||||
| Sulfur relay | 9.24 × 10−3 | ||||||
| Transporters | 1.53 × 10−11 | ||||||
| 10 | 62 | NS | 8.36 × 10−21 | Prokaryotic defense system | 2.24 × 10−2 | NS | |
| 11 | 55 | NS | 5.65 × 10−30 | Starch and sucrose metabolism | 6.06 × 10−6 | GH5 | 9.18 × 10−3 |
| GH9 | 1.02 × 10−4 | ||||||
| GH45 | 1.43 × 10−2 | ||||||
| 12 | 45 | 6.31 × 10−03 | 4.48 × 10−10 | NS | GH16 | 7.20 × 10−3 | |
| 13 | 44 | 5.55 × 10−16 | 1.96 × 10−31 | Chaperones and folding catalysts | 7.28 × 10−3 | NS | |
| 14 | 38 | NS | NS | NS | NS | ||
| 15 | 29 | 2.41 × 10−07 | 6.78 × 10−10 | Carbohydrate metabolism | 7.48 × 10−4 | CBM35 | 3.32 × 10−9 |
| GH43 | 9.59 × 10−9 | ||||||
| 16 | 27 | 2.47 × 10−18 | 3.37 × 10−13 | Carbohydrate metabolism | 1.87 × 10−2 | CBM6 | 1.03 × 10−9 |
| CE6 | 6.30 × 10−5 | ||||||
| Pentose and glucuronate interconversions | 7.42 × 10−3 | GH10 | 1.98 × 10−4 | ||||
| GH30 | 2.76 × 10−5 | ||||||
| PL1 | 1.99 × 10−6 | ||||||
| 17 | 21 | 3.47 × 10−14 | 3.71 × 10−13 | Galactose metabolism | 6.87 × 10−3 | CBM6 | 3.50 × 10−20 |
| Glycerolipid metabolism | 3.98 × 10−2 | GH27 | 4.71 10−2 | ||||
| Glycosphingolipid biosynthesis | 1.35 × 10−2 | GH43 | 9.91 × 10−10 | ||||
| Other glycan degradation | 6.45 × 10−4 | GH95 | 4.71 × 10−2 | ||||
| Sphingolipid metabolism | 6.45 × 10−4 | GH141 | 4.71 × 10−2 | ||||
Values for growth rate, substrate, KEGG Category, and CAZy category are P values, after adjusting for multiple comparisons (hypergeometric test, Holm’s correction [33])
NS not significant