| Predictions |
---|
 | Not ChIP-chip | ChIP-chip | Total | Recall | Precision |
---|
FNR
| Â | Â | Â | Â | Â |
ChIP-chip | - | 73 | 73 | Â | Â |
CLR | 14 | 0 | 14 | 0 | 0 |
SEREND | 76 | 19 | 95 | 0.26 | 0.20 |
DISTILLER | 21 | 4 | 25 | 0.055 | 0.16 |
CRP
| Â | Â | Â | Â | Â |
ChIP-chip | - | 57 | 57 | Â | Â |
CLR | 23 | 0 | 23 | 0 | 0 |
SEREND | 203 | 9 | 212 | 0.16 | 0.042 |
DISTILLER | 57 | 6 | 63 | 0.11 | 0.095 |
Fis
| Â | Â | Â | Â | Â |
ChIP-chip | - | 179 | 179 | Â | Â |
CLR | 59 | 4 | 63 | 0.022 | 0.06 |
SEREND | 33 | 4 | 37 | 0.022 | 0.11 |
DISTILLER | 17 | 3 | 20 | 0.017 | 0.15 |
H-NS
| Â | Â | Â | Â | Â |
ChIP-chip | - | 82 | 82 | Â | Â |
CLR | 26 | 0 | 26 | 0 | 0 |
SEREND | 4 | 0 | 4 | 0 | 0 |
DISTILLER | 0 | 0 | 0 | 0 | 0 |
IHF
| Â | Â | Â | Â | Â |
ChIP-chip | - | 110 | 110 | Â | Â |
CLR | 67 | 4 | 71 | 0.036 | 0.056 |
SEREND | 79 | 10 | 89 | 0.091 | 0.11 |
DISTILLER | 14 | 4 | 18 | 0.036 | 0.22 |
- For each method, the identified interactions that were novel as compared to RegulonDB were selected. For all novel interactions, we indicate whether (ChIP-chip) or not (Not ChIP-chip) the interactions were found in a corresponding ChIP-chip experiment. The recall (TP/TP + FN) and precision (TP/TP + FP) were calculated using the ChIP-chip data as a gold standard. Interactions identified by either CLR, SEREND or DISTILLER and confirmed by a ChIP-chip experiment were considered to be true positives (TP); interactions confirmed by a ChIP-chip experiment but not identified by either CLR, SEREND or DISTILLER were considered false negatives (FN); interactions identified by either CLR, SEREND or DISTILLER but not confirmed in a ChIP-chip experiment were considered false positives (FP).