Table 1.
Comparison of discriminative motif finding methods on the yeast dataset
| TF | DECOD | DME | DEME | CMF | Seeder | ALSE | Width | Enrichment |
|---|---|---|---|---|---|---|---|---|
| ABF1 | + | + | + | + | + | 13 | 99 | |
| CBF1 | + | + | + | + | + | 7 | 99 | |
| FHL1 | + | + | + | + | + | 10 | 99 | |
| RAP1 | + | + | + | + | 10 | 79.92 | ||
| REB1 | + | + | + | + | + | 7 | 77.93 | |
| UME6 | + | + | + | + | + | 8 | 72.32 | |
| RPN4 | 9 | 72.02 | ||||||
| GCN4 | + | + | + | + | + | 7 | 64.62 | |
| YAP7 | 8 | 62.65 | ||||||
| MCM1 | + | + | 11 | 55.28 | ||||
| NRG1 | + | 7 | 45.42 | |||||
| MBP1 | + | + | + | + | + | 7 | 40 | |
| SKN7 | + | 9 | 38.79 | |||||
| CIN5 | + | + | + | 8 | 38.36 | |||
| SUM1 | + | + | + | + | 10 | 36.47 | ||
| SWI6 | + | + | + | + | + | 7 | 33.62 | |
| HSF1 | + | 13 | 32.96 | |||||
| SWI4 | + | + | + | + | + | 7 | 31.96 | |
| TYE7 | + | + | + | + | + | + | 8 | 30.56 |
| SFP1 | 9 | 26.64 | ||||||
| FKH2 | + | + | + | + | 7 | 26.62 | ||
| Total (Top) | 15 | 13 | 15 | 14 | 11 | 3 | ||
| Total (All) | 28 | 31 | 34 | 24 | 17 | 9 |
+: Correctly recover the known motif.
Total (Top): the total number of the top 21 motifs with enrichment score ≥25 correctly recovered by each method.
Total (All): the total number of all motifs correctly recovered by each method (see Results in Supplementary Materials for details).