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.
| Pathway | Genes | Edges | C | Super Pathway |
|---|---|---|---|---|
| Photosynthesis, light reaction | 10 | 40 | 0.923 | PME |
| Carotenoid biosynthesis | 10 | 22 | 0.754 | B |
| Gly degradation I | 8 | 10 | 0.604 | D/U/A |
| tRNA charging pathway | 44 | 102 | 0.412 | B |
| Calvin cycle | 36 | 93 | 0.399 | D/U/A |
| Photorespiration | 29 | 42 | 0.318 | PME |
| Chlorophyll biosynthesis | 49 | 105 | 0.298 | B |
| Gluconeogenesis | 55 | 82 | 0.288 | B |
| Fru degradation (anaerobic) | 57 | 57 | 0.266 | D/U/A |
| Glycolysis I | 59 | 57 | 0.257 | PME |
| Sorbitol fermentation | 59 | 57 | 0.257 | PME |
| Glycolysis IV | 59 | 57 | 0.257 | PME |
| Acetate fermentation | 60 | 57 | 0.252 | PME |
| De novo biosynthesis of purine nucleotides II | 29 | 22 | 0.22 | B |
| Starch biosynthesis | 19 | 7 | 0.211 | B |
| Fatty acid biosynthesis—initial steps | 30 | 13 | 0.156 | B |
| De novo biosynthesis of purine nucleotides I | 46 | 32 | 0.151 | B |
| TCA cycle—aerobic respiration | 42 | 11 | 0.111 | PME |
| Acetyl-CoA assimilation | 28 | 6 | 0.107 | PME |
| Colanic acid building blocks biosynthesis | 53 | 12 | 0.066 | B |