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Table 1 Biological validation of LeMoNe on E. coli

From: Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

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
  1. 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.