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.