Table 3.
Enrichment of the PPI subnets (Coum, SN.1 ~ SN9; Syr, SN.10 ~ SN.11; Fer, SN.12 ~ SN.13; Van, SN.14 ~ SN.16)
| Subnet | Enrichment itema | Function annotation | FDR |
|---|---|---|---|
| SN.1 | BP GO:0044267 | Cellular protein metabolic process | 8.85E − 38 |
| MF GO:0003735 | Structural constituent of ribosome | 5.39E − 33 | |
| CC GO:0005840 | Ribosome | 4.22E − 33 | |
| KEGG cac03010 | Ribosome | 3.87E − 35 | |
| UniProt KW-0687 | Ribonucleoprotein | 1.82E − 35 | |
| SN.2 | BP GO:0006261 | DNA-dependent DNA replication | 4.78E − 02 |
| SN.3 | KEGG cac02040 | Flagellar assembly | 1.15E − 23 |
| UniProt KW-0282 | Flagellum | 5.41E − 17 | |
| SN.4 | BP GO:0006281 | DNA repair | 6.64E − 06 |
| MF GO:0140097 | Catalytic activity, acting on DNA | 3.03E − 02 | |
| CC GO:1990391 | DNA repair complex | 4.70E − 03 | |
| KEGG cac03440 | Homologous recombination | 1.70E − 03 | |
| UniProt KW-0234 | DNA repair | 2.15E − 07 | |
| SN.5 | CC GO:0005737 | Cytoplasm | 2.03E − 02 |
| KEGG cac01230 | Biosynthesis of amino acids | 2.70E − 03 | |
| SN.6 | BP GO:0090304 | Nucleic acid metabolic process | 8.50E − 04 |
| MF GO:0008144 | Drug binding | 8.97E − 05 | |
| CC GO:0005737 | Cytoplasm | 9.30E − 03 | |
| KEGG cac00970 | Aminoacyl-tRNA biosynthesis | 1.20E − 03 | |
| UniProt KW-0030 | Aminoacyl-tRNA synthetase | 1.20E − 03 | |
| SN.7 | KEGG cac00523 | Polyketide sugar unit biosynthesis | 6.80E − 04 |
| UniProt KW-0808 | Transferase | 5.10E − 03 | |
| SN.8 | KEGG cac01130 | Biosynthesis of antibiotics | 3.56E − 06 |
| UniProt KW-0501 | Molybdenum cofactor biosynthesis | 2.06E − 02 | |
| SN.9 | UniProt KW-0418 | Kinase | 6.50E − 04 |
| SN.10 | BP GO:0034645 | Cellular macromolecule biosynthetic process | 9.66E − 13 |
| MF GO:0003735 | Structural constituent of ribosome | 2.38E − 13 | |
| CC GO:0005840 | Ribosome | 2.08E − 13 | |
| KEGG cac03010 | Ribosome | 1.15E − 13 | |
| SN.11 | KEGG cac00500 | Starch and sucrose metabolism | 5.14E − 06 |
| UniProt KW-0732 | Signal | 8.54E − 09 | |
| SN.12 | None | ||
| SN.13 | UniProt KW-0808 | Transferase | 4.20E − 02 |
| SN.14 | BP GO:0009260 | Ribonucleotide biosynthetic process | 3.64E − 06 |
| MF GO:0016879 | Ligase activity, forming carbon–nitrogen bonds | 8.81E − 07 | |
| KEGG cac00230 | Purine metabolism | 8.75E − 13 | |
| UniProt KW-0658 | Purine biosynthesis | 1.76E − 17 | |
| SN.15 | BP GO:0030435 | Sporulation resulting in formation of a cellular spore | 3.17E − 05 |
| MF GO:0016987 | Sigma factor activity | 5.00E − 04 | |
| UniProt KW-0749 | Sporulation | 6.55E − 06 | |
| SN.16 | BP GO:1901564 | Organonitrogen compound metabolic process | 2.30E − 03 |
| MF GO:0016758 | Transferase activity, transferring hexosyl groups | 6.30E − 03 | |
| KEGG cac00400 | Phenylalanine, tyrosine and tryptophan biosynthesis | 5.52E − 05 | |
| UniProt KW-0133 | Cell shape | 2.51E − 06 |
aThe genes in each subnet were enriched in GO, KEGG and UniProt databases, and the items with minimum FDR (< 0.05) was listed