Table III. Functional group enrichment of the PG network produced by MetaOmGraph.
| Functional Group | Bin Sizea | Whole Networkb | Module 1b | Module 2b | Module 3b | Module 4b |
| Protein degradation | 1,355 | 0.1 | 0.1 | 0.2 | 0.1 | 0.1 |
| Plastid | 42 | 3.3 | 1.2 | 6.5 | 3.3 | 3.6 |
| Not plastid | 1,313 | 0.0 | 0.1 | 0.0 | 0.0 | 0.0 |
| Core PG | 25 | 3.4 | 4.0 | 4.5 | 4.8 | 2.0 |
| Light reaction | 139 | 0.8 | 0.4 | 0.5 | 1.4 | 1.1 |
| Light stress-Lil/Sep/Ohp | 8 | 0.5 | 0.0 | 1.6 | 0.0 | 0.0 |
| NDH dependent and independent, Immutans, PIFI | 29 | 1.5 | 1.7 | 0.4 | 2.8 | 0.0 |
| PSI, PSII, ATPsynt, Cytb6f, FNR, electron carriers (PC, Fd) | 94 | 0.5 | 0.0 | 0.3 | 0.9 | 1.6 |
| Thylakoid-bound regulators, including kinases and phosphatases | 5 | 3.2 | 0.0 | 5.0 | 8.0 | 0.0 |
| Isoprenoid metabolism | 124 | 0.7 | 0.2 | 1.6 | 0.5 | 0.4 |
| Plastid | 59 | 1.1 | 0.0 | 2.5 | 1.0 | 0.8 |
| Not plastid | 65 | 0.3 | 0.4 | 0.8 | 0.0 | 0.0 |
| Redox | 187 | 0.7 | 0.4 | 0.3 | 2.5 | 0.3 |
| Tetrapyrrole metabolism | 50 | 0.5 | 2.0 | 0.0 | 0.4 | 0.0 |
| Stress | 690 | 0.1 | 0.1 | 0.1 | 0.0 | 0.0 |
| Miscellaneous | 1,274 | 0.1 | 0.2 | 0.1 | 0.1 | 0.1 |
| Protein, other | 1,535 | 0.1 | 0.0 | 0.1 | 0.1 | 0.4 |
| Plastid | 211 | 0.7 | 0.0 | 0.8 | 0.4 | 2.8 |
| Not plastid | 1,326 | 0.0 | 0.1 | 0.0 | 0.0 | 0.0 |
| Not assigned | 7,707 | 0.1 | 0.1 | 0.1 | 0.1 | 0.0 |
| Development | 521 | 0.1 | 0.2 | 0.1 | 0.0 | 0.0 |
| CHO metabolismc | 441 | 0.3 | 0.0 | 0.2 | 0.2 | 0.9 |
| Transport | 944 | 0.1 | 0.1 | 0.1 | 0.0 | 0.1 |
| Otherd | 2,128 | 0.1 | 0.1 | 0.0 | 0.0 | 0.0 |
| Signaling | 1,048 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| Lipid metabolism | 331 | 0.0 | 0.1 | 0.0 | 0.0 | 0.0 |
| DNA/RNA | 2,659 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
Number of genes (represented by a single probe spot on the 22K Affymetrix microarray chip) in each bin.
Number of edges per bin, normalized for bin size and normalized for number of PG core genes per module. Values in boldface are enriched functions.
Includes major and minor carbohydrate metabolism, gluconeogenesis, glycolysis, tricarboxylic acid cycle, C1 metabolism, fermentation, oxidative pentose phosphate pathway, Calvin cycle, and all other dark reactions.
Includes cofactor and vitamin metabolism, metal handling, xenobiotics, amino acid metabolism, nucleotide metabolism, cytoskeleton, mitochondrial electron transport, cell wall, cell, cell division, cell cycle, nitrogen metabolism, photorespiration, polyamine metabolism, sulfur assimilation, secondary metabolism (excluding isoprenoids/tetrapyrrole), and hormone metabolism.