Table 1.
Biological validation of LeMoNe on E. coli
| Regulator | Module ID | Score | Target enrich. | Autoreg. | Pathway | Local | Function |
| gatR_2 | 73 | 1912.98 | ** | * | ** | carbon utilization > carbon compounds | |
| gadE | 48 | 1844.50 | ** | * | * | ** | adaptations > pH |
| gutM | 38 | 1807.24 | ** | * | * | * | carbon utilization > carbon compounds |
| ymfN | 58 | 1749.11 | * | ||||
| ymfN | 33 | 1711.17 | * | ||||
| fliA | 12 | 1510.48 | ** | * | * | ** | motility, chemotaxis, energytaxis; flagella; biosynthesis of flagellum |
| rcsB | 62 | 1261.72 | * | * | biosynthesis of colanic acid (M antigen) | ||
| fecI | 57 | 1200.77 | * | * | adaptations > Fe aquisition | ||
| gatR_2 | 42 | 1176.55 | ** | * | ** | carbon utilization > carbon compounds | |
| yahA | 82 | 1171.92 | |||||
| rcsA | 87 | 1151.97 | ** | * | * | biosynthesis of colanic acid (M antigen) | |
| lexA | 20 | 996.62 | ** | * | * | * | SOS response; DNA repair; protection > radiation |
| lldR | 65 | 976.84 | ** | * | * | * | energy metabolism; aerobic respiration |
| fliA | 45 | 956.70 | ** | * | * | motility, chemotaxis, energytaxis | |
| fliA | 18 | 903.46 | * | * | * | biosynthesis of flagellum; motility, chemotaxis, energytaxis; flagella | |
| nac | 85 | 827.17 | * | * | nitrogen metabolism | ||
| yiaG | 15 | 816.55 | |||||
| ydaK | 23 | 815.75 | ** | ||||
| ydaK | 154 | 805.22 | |||||
| fnr | 23 | 798.27 | * | * | * | ** | energy metabolism; anaerobic respiration; membrane |
| lrp | 5 | 777.80 | * | * | biosynthesis of building blocks > amino acids | ||
| araC | 46 | 760.44 | ** | * | * | ** | carbon utilization > carbon compounds |
| appY | 50 | 748.75 | |||||
| yfiE | 67 | 736.50 | |||||
| osmE | 15 | 734.87 | |||||
| lexA | 78 | 726.67 | ** | * | * | SOS response | |
| purR | 144 | 708.63 | * | * | |||
| uidR | 81 | 708.36 | * | ||||
| araC | 21 | 678.10 | * | * | * | carbon utilization > carbon compounds | |
| yfeG | 29 | 663.94 | |||||
| b1450 | 53 | 662.16 | |||||
| flhC | 18 | 650.64 | ** | * | biosynthesis of flagellum; motility, chemotaxis, energytaxis; flagella | ||
| ogrK | 83 | 645.35 | |||||
| fliA | 17 | 637.28 | * | ||||
| rpoS | 14 | 637.13 | ** | * | * | adaptations > osmotic pressure | |
| pdhR | 55 | 633.52 | * | * | energy metabolism; anaerobic respiration | ||
| tdcA | 31 | 619.06 | * | * | * | * | threonine catabolism; carbon utilization > amino acids |
| yebK | 106 | 617.44 | |||||
| araC | 56 | 608.17 | ** | * | * | carbon utilization > carbon compounds | |
| csgD | 26 | 599.30 | * | ||||
| hycA | 66 | 596.27 | |||||
| tdcR | 11 | 593.75 | * | carbon utilization > amino acids | |||
| fliA | 24 | 593.05 | * | * | * | flagella; motility, chemotaxis, energytaxis; biosynthesis of flagellum | |
| chbR | 24 | 590.31 | * | ||||
| hycA | 29 | 563.45 | * | ||||
| galS | 76 | 561.25 | ** | * | * | ** | carbon utilization > carbon compounds |
| nlp | 77 | 559.41 | |||||
| yfeC | 119 | 549.33 | |||||
| b1506 | 36 | 548.33 | |||||
| lrp | 10 | 528.90 | * | * | * | biosynthesis of building blocks > amino acids | |
| cspB | 37 | 527.86 | |||||
| cusR | 68 | 515.56 | ** | * | * | ** | extrachromosomal > transposon related |
| b1284 | 51 | 514.78 | |||||
| nanR | 9 | 508.87 | |||||
| yohL | 90 | 496.21 | |||||
| lrp | 126 | 493.60 | * | * | biosynthesis of building blocks > amino acids | ||
| yjjQ | 179 | 491.02 | |||||
| yehV | 63 | 483.29 | |||||
| ogrK | 27 | 481.75 | |||||
| slyA | 3 | 474.43 | |||||
| ydcN | 16 | 467.66 | |||||
| cpxR | 9 | 465.39 | * | * | * | adaptations > other (mechanical, nutritional, oxidative stress) | |
| yehV | 34 | 451.77 | |||||
| fruR | 63 | 449.25 | |||||
| araC | 64 | 441.57 | * | * | * | carbon utilization > carbon compounds | |
| fis | 19 | 436.12 | ** | * | * | * | information transfer > RNA related > tRNA |
| fadR | 16 | 435.98 | * | ||||
| purR | 10 | 431.78 | ** | * | * | biosynthesis of building blocks > nucleotides | |
| cadC | 37 | 429.32 | * | ||||
| fecI | 54 | 429.28 | * | ||||
| rstA | 102 | 428.94 | |||||
| tdcR | 61 | 428.84 | |||||
| flhC | 24 | 426.88 | ** | * | * | flagella; motility, chemotaxis, energytaxis; biosynthesis of flagellum |
Biological validation of the LeMoNe 30% precision network for E. coli. Target enrichment: (*) module is enriched in known targets of the predicted regulator, (**) module is most enriched for predicted regulator. Autoregulator: (*) regulator is an autoregulator. Pathway: (*) module is enriched in the same function(s) as the regulator. Local: (*) regulator is in the same operon as the module genes, (**) Transcription unit of regulator is adjacent to transcription units of the module genes. Function: enriched functions of the module. Regulators in bold face are putative regulators without known targets; module IDs in bold face consist only of uncharacterized genes.