Table III. Functional group enrichment of the PG network produced by MetaOmGraph
Functional GroupBin SizeaWhole NetworkbModule 1bModule 2bModule 3bModule 4b
Protein degradation1,3550.10.10.20.10.1
 Plastid423.31.26.53.33.6
 Not plastid1,3130.00.10.00.00.0
Core PG253.44.04.54.82.0
Light reaction1390.80.40.51.41.1
 Light stress-Lil/Sep/Ohp80.50.01.60.00.0
 NDH dependent and independent, Immutans, PIFI291.51.70.42.80.0
 PSI, PSII, ATPsynt, Cytb6f, FNR, electron carriers (PC, Fd)940.50.00.30.91.6
 Thylakoid-bound regulators, including kinases and phosphatases53.20.05.08.00.0
Isoprenoid metabolism1240.70.21.60.50.4
 Plastid591.10.02.51.00.8
 Not plastid650.30.40.80.00.0
Redox1870.70.40.32.50.3
Tetrapyrrole metabolism500.52.00.00.40.0
Stress6900.10.10.10.00.0
Miscellaneous1,2740.10.20.10.10.1
Protein, other1,5350.10.00.10.10.4
 Plastid2110.70.00.80.42.8
 Not plastid1,3260.00.10.00.00.0
Not assigned7,7070.10.10.10.10.0
Development5210.10.20.10.00.0
CHO metabolismc4410.30.00.20.20.9
Transport9440.10.10.10.00.1
Otherd2,1280.10.10.00.00.0
Signaling1,0480.00.00.00.00.0
Lipid metabolism3310.00.10.00.00.0
DNA/RNA2,6590.00.00.00.00.0
  • a Number of genes (represented by a single probe spot on the 22K Affymetrix microarray chip) in each bin.

  • b 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.

  • c 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.

  • d 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.