Table 3.
Performance comparison of 10 motif finders on 28 regulons. PRISM and nine popular motif finders where run on the SCPD regulons. The data are summarized as in Table 2. The programs tested were: PRISM, RSAT, Mitra [39], AlignACE [40], MotifSampler (MS) [41], BioProspector (BioProsp) [42], MEME [43], Consensus [44], Weeder [45] and Yeast Motif Finder (YMF) [4]. Some programs did not return values for MCM1, so this regulon was omitted.
| PRISM | RSAT | Mitra | AlignACE | MS | BioProsp | MEME | Consensus | Weeder | YMF | |
| BAS1 | 0.07 | 0.36 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.20 | 0.36 |
| CPF1 | 0.62 | 0.00 | 0.00 | 0.54 | 0.00 | 0.62 | 0.48 | 0.00 | 0.47 | 0.44 |
| CSRE | 0.09 | 0.25 | 0.00 | 0.10 | 0.00 | 0.49 | 0.30 | 0.00 | 0.08 | 0.07 |
| GATA | 0.73 | 0.73 | 0.21 | 0.18 | 0.39 | 0.13 | 0.19 | 0.00 | 0.29 | 0.56 |
| GCN4 | 0.50 | 0.29 | 0.02 | 0.26 | 0.28 | 0.00 | 0.02 | 0.00 | 0.37 | 0.29 |
| GCR1 | 0.12 | 0.24 | 0.18 | 0.04 | 0.05 | 0.10 | 0.08 | 0.25 | 0.08 | 0.10 |
| GLN3 | 0.00 | 0.00 | 0.02 | 0.79 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 |
| HAP2 | 0.11 | 0.00 | 0.02 | 0.07 | 0.00 | 0.18 | 0.00 | 0.00 | 0.01 | 0.00 |
| MATA1 | 0.19 | 0.10 | 0.26 | 0.17 | 0.00 | 0.49 | 0.12 | 0.00 | 0.06 | 0.13 |
| MATA2 | 0.43 | 0.28 | 0.08 | 0.15 | 0.04 | 0.24 | 0.09 | 0.00 | 0.25 | 0.23 |
| MCB | 0.69 | 0.62 | 0.02 | 0.40 | 0.48 | 0.05 | 0.26 | 0.51 | 0.50 | 0.64 |
| MIG1 | 0.01 | 0.22 | 0.02 | 0.14 | 0.02 | 0.16 | 0.21 | 0.18 | 0.13 | 0.29 |
| PDR3 | 0.71 | 0.46 | 0.51 | 0.76 | 0.75 | 0.42 | 0.37 | 0.73 | 0.82 | 0.74 |
| PHO2 | 0.01 | 0.00 | 0.06 | 0.08 | 0.00 | 0.10 | 0.00 | 0.01 | 0.01 | 0.00 |
| PHO4 | 0.25 | 0.21 | 0.24 | 0.23 | 0.00 | 0.21 | 0.33 | 0.23 | 0.00 | 0.18 |
| RAP1 | 0.18 | 0.18 | 0.26 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.24 | 0.18 |
| REB1 | 0.32 | 0.36 | 0.00 | 0.01 | 0.47 | 0.30 | 0.36 | 0.00 | 0.26 | 0.36 |
| ROX1 | 0.19 | 0.33 | 0.05 | 0.05 | 0.00 | 0.09 | 0.45 | 0.00 | 0.17 | 0.18 |
| RPA | 0.02 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.00 | 0.00 | 0.00 |
| SCB | 0.69 | 0.52 | 0.58 | 0.08 | 0.00 | 0.09 | 0.40 | 0.00 | 0.57 | 0.50 |
| SFF | 0.02 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| STE12 | 0.57 | 0.65 | 0.08 | 0.24 | 0.00 | 0.00 | 0.42 | 0.00 | 0.37 | 0.50 |
| TBP | 0.00 | 0.00 | 0.03 | 0.00 | 0.19 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 |
| UASCAR | 0.07 | 0.04 | 0.11 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.02 | 0.02 |
| UASH | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| UASPHR | 0.03 | 0.06 | 0.04 | 0.10 | 0.00 | 0.03 | 0.07 | 0.09 | 0.10 | 0.03 |
| UIS | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 | 0.10 | 0.09 | 0.01 |
| URS1H | 0.60 | 0.42 | 0.62 | 0.00 | 0.50 | 0.75 | 0.41 | 0.46 | 0.38 | 0.40 |
| Average Φ | 0.26 | 0.23 | 0.13 | 0.16 | 0.11 | 0.17 | 0.17 | 0.09 | 0.20 | 0.22 |
| Wins | 6 | 1.5 | 3 | 2 | 2 | 6 | 2 | 1 | 1 | 1.5 |
| # ≥ 0.50 | 8 | 4 | 3 | 3 | 1 | 2 | 0 | 2 | 3 | 5 |
| # ≥ 0.33 | 9 | 9 | 3 | 4 | 5 | 5 | 7 | 3 | 7 | 9 |
| # ≥ 0.10 | 17 | 17 | 10 | 12 | 7 | 14 | 13 | 6 | 14 | 17 |
| clear win for PRISM | 8 | 11 | 11 | 14 | 9 | 12 | 13 | 10 | 8 | |
| clear loss for PRISM | 5 | 0 | 2 | 2 | 4 | 3 | 2 | 3 | 2 | |