Table 2  Out of 206 gene/TF interactions found in the RegulonDB (Salgado et al. 2004) and EcoCyc databases, 44 scored higher than the imposed threshold.
TF  Gene  Final Score  predicted sign  actual sign
1  ArcA-Phosphorylated  yfiD  1.670768591  up  up
2  ArgR-L-arginine  argG  2.624262246  down  down
3  CRP-cAMP  ugpQ  2.085693237  up  up
4  CRP-cAMP  ugpC  1.438960585  up  up
5  CRP-cAMP  ugpB  1.527292985  up  up
6  CRP-cAMP  rhaB  2.909109432  up  up
7  CRP-cAMP  cytR  2.119101207  up  up
8  CRP-cAMP  fis  1.887330412  up/down  up/down
9  FhlA-Formate  hyfA  2.509458668  up  up
10  Fis  relA  1.595459732  up  up
11  GntR  idnK  1.591861262  down  down
12  Lrp  livJ  1.380451883  down  down
13  MalT-Maltotriose-ATP  malZ  1.44543234  up  up
14  NarL-Phosphorylated  fdhF  2.059069186  up  up
15  NtrC-Phosphorylated  astC  2.256990592  up  up
16  ArgR-L-arginine  astC  1.505034  down  up
17  CRP-cAMP  nagE  1.501987378  up/down  up
18  CRP-cAMP  rpoS  2.319114034  up/down  down
19  OmpR-Phosphorylated  nmpC  1.572242248  up  down
20  ArcA-Phosphorylated  aceE  1.998375233  down  down
21  ArcA-Phosphorylated  appC  2.066734924  up  up
22  CRP-cAMP  entC  2.93996178  up  up
23  CRP-cAMP  fepA  3.821927836  up  up
24  CRP-cAMP  fumA  3.496049117  up  up
25  CRP-cAMP  gadB  2.197333426  down  down
26  CRP-cAMP  galP  2.37334941  up  up
27  CRP-cAMP  gapA  1.811986697  up  up
28  CRP-cAMP  ompF  1.315706561  up  up
29  FruR  acnA  1.633652931  up  up
30  FruR  glk  2.112996214  down  down
31  GadE  gadB  1.973757857  up  up
32  Hns  gadB  1.78680429  down  down
33  LexA  uvrC  1.590391147  down  down
34  MetJ-S-adenosylmethionine  metE  3.264214502  down  down
35  MetJ-S-adenosylmethionine  metR  1.611151228  down  down
36  MetR-Homocysteine  metE  3.45265202  up  up
37  PhoP-Phosphorylated  rstA  1.6475787  up  up
38  CRP-cAMP  prpR  3.147648347  up/down  up
39  Fnr  fdhF  1.985483486  up/down  up
40  CRP-cAMP  nagE  1.501987378  up/down  up
41  NarP-Phosphorylated  fdhFp  1.645007039  up/down  up
42  NarP-Phosphorylated  fdnG  2.778075473  up/down  down
43  Fnr  dcuS  1.359810967  down  up
44  Fnr  purM  1.427076396  up  down
The p-value (using binary distribution) is found to be less than 1.0e-50.