Table 1.
Pathway analysis of Ab genes differentially expressed in PgAb communities
| Pathway Name | Genes UP | Genes DOWN | FDR1 |
|---|---|---|---|
| Aminoacyl-tRNA biosynthesis | 27 | 1 | 6.31E-06 |
| One carbon pool by folate | 11 | 1 | 0.000476599 |
| Fatty acid biosynthesis | 13 | 1 | 0.000569961 |
| Sulfur metabolism | 14 | 16 | 0.001322774 |
| Pyrimidine metabolism | 36 | 2 | 0.001330085 |
| Glycine, serine and threonine metabolism | 24 | 8 | 0.002933338 |
| Lysine biosynthesis | 12 | 4 | 0.006448065 |
| Purine metabolism | 47 | 21 | 0.007516597 |
| Phenylalanine, tyrosine and tryptophan biosynthesis | 21 | 2 | 0.008386424 |
| Peptidoglycan biosynthesis | 18 | 1 | 0.008877038 |
| Fructose and mannose metabolism | 8 | 2 | 0.011766396 |
| Cysteine and methionine metabolism | 21 | 8 | 0.011981639 |
| Methane metabolism | 15 | 4 | 0.013718309 |
| Vitamin B6 metabolism | 5 | 1 | 0.013718309 |
| Novobiocin biosynthesis | 4 | 0 | 0.025871218 |
| Arginine and proline metabolism | 12 | 5 | 0.025871218 |
| Propanoate metabolism | 27 | 10 | 0.030004433 |
| Pyruvate metabolism | 29 | 13 | 0.030004433 |
| Biotin metabolism | 10 | 3 | 0.030004433 |
| Amino sugar and nucleotide sugar metabolism | 14 | 5 | 0.035195636 |
| Oxidative phosphorylation | 35 | 4 | 0.04482427 |
| Folate biosynthesis | 11 | 8 | 0.04482427 |
| Tyrosine metabolism | 6 | 8 | 0.04482427 |
| Arginine biosynthesis | 11 | 9 | 0.047789592 |
1
Pathway analysis was performed using the Bioconductor package and pathways were considered significant with a false-discovery rate (FDR) < 0.05