Table 3 Evaluation on the phylogenetic footprinting datasets from γ-proteobacterial genomes using the predictions in the E. coli K12 genome
From: MotifClick: prediction of cis-regulatory binding sites via merging cliques
| Â | Â | Top 1 | Top 5 | Top 10 | Top 15 | Top 20 |
|---|---|---|---|---|---|---|
MotifClick | BS (MF) | 331 (85) | 793 (108) | 1055 (114) | 1186 (114) | 1262 (117) |
| Â | PS (lbSp) | 2575 (0.129) | 7706 (0.103) | 11056 (0.095) | 12779 (0.093) | 13592 (0.093) |
MEME | BS (MF) | 298 (83) | 877 (109) | 1134 (115) | 1202 (117) | 1233 (117) |
| Â | PS (lbSp) | 3352 (0.089) | 14243 (0.062) | 20999 (0.054) | 23912 (0.050) | 25412 (0.049) |
MotifCut | BS (MF) | 241 (75) | 487 (89) | 544 (96) | 640 (102) | 744 (107) |
| Â | PS (lbSp) | 1942 (0.124) | 4763 (0.102) | 6552 (0.083) | 9145 (0.070) | 10408 (0.071) |
BioProspecter | BS (MF) | 354 (85) | 743 (102) | 953 (112) | 1056 (112) | 1150 (116) |
| Â | PS (lbSp) | 4950 (0.072) | 7678 (0.097) | 10090 (0.107) | 11287 (0.094) | 12306 (0.093) |
MotifClick + MEME | BS (MF) | 474 (98) | 1029 (114) | 1259 (118) | 1335 (120) | 1357 (120) |
MEME + BioProspector | BS (MF) | 472 (92) | 1051 (115) | 1258 (118) | 1312 (119) | 1339 (119) |