Appendix 2—table 1. A suite of experimentally validated and high-evidence binding sites used to test our automated binding site finding algorithm.
Specifically, this list of genes was used to test the false negative rate of our Reg-Seq method by examining what fraction of high-evidence sites were also identified with Reg-Seq.
| Gene | Transcription factor | Transcription factor type |
|---|---|---|
| rspA | CRP | activator |
| rspA | YdfH | repressor |
| araAB | AraC (two sites) | activator |
| znuCB | Zur | repressor |
| xylA | CRP | activator |
| xylA | XylR (two sites) | activator |
| xylF | XylR (two sites) | activator |
| dicC | DicA | repressor |
| relBE | RelBE | repressor |
| ftsK | LexA | repressor |
| znuA | Zur | repressor |
| lac | CRP | activator |
| marR | Fis | activator |
| marR | MarA | activator |
| marR | MarR (two sites) | repressor |
| dgoR | CRP | activator |
| dgoR | DgoR (right site) | repressor |
| ompR | IHF (three sites) | repressor |
| ompR | CRP | repressor |
| dicA | DicA | repressor |
| araC | AraC (two sites) | repressor |
| araC | AraC (two sites) | activator |
| araC | CRP | activator |
| araC | XylR (two sites) | repressor |