Table II.

Most highly coexpressed pathways

Pathways with unusually high levels of coexpression (empirically determined pathway p value < 0.0001) and at least five coexpression links (edges) between genes are listed. The column labeled Genes gives the number of genes per pathway included in the coexpression analysis. The column labeled Edges lists the number of coexpression links in the within-pathway coexpression network, using coexpression cutoff 1E-80. C is the clustering coefficient for the coexpression network; larger values for C indicate a higher degree of connectivity (Watts and Strogatz, 1998). Super-pathway designations are from AraCyc: PME, Generation of precursor metabolites and energy; B, biosynthesis; D/U/A, degradation/utilization/assimilation.

PathwayGenesEdgesCSuper Pathway
Photosynthesis, light reaction10400.923PME
Carotenoid biosynthesis10220.754B
Gly degradation I8100.604D/U/A
tRNA charging pathway441020.412B
Calvin cycle36930.399D/U/A
Photorespiration29420.318PME
Chlorophyll biosynthesis491050.298B
Gluconeogenesis55820.288B
Fru degradation (anaerobic)57570.266D/U/A
Glycolysis I59570.257PME
Sorbitol fermentation59570.257PME
Glycolysis IV59570.257PME
Acetate fermentation60570.252PME
De novo biosynthesis of purine nucleotides II29220.22B
Starch biosynthesis1970.211B
Fatty acid biosynthesis—initial steps30130.156B
De novo biosynthesis of purine nucleotides I46320.151B
TCA cycle—aerobic respiration42110.111PME
Acetyl-CoA assimilation2860.107PME
Colanic acid building blocks biosynthesis53120.066B