Table 1.
Performances of our method and some other motif finding methods in comparison to experimentally defined binding sites
| TF | Our method |
Other methods |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
a = 1, b = 2 |
a = 1, b = 1 |
a = 0, b = 1 |
a = 1, b = 0 |
a = 0, b = 0 |
AlignACE |
BioProspector |
SPACER |
|||||||||
| Sim. | Rank | Sim. | Rank | Sim. | Rank | Sim. | Rank | Sim. | Rank | Sim. | Rank | Sim. | Rank | Sim. | Rank | |
| ABF1* | 89.7 | 1 | 89.7 | 1 | 89.7 | 1 | 89.0 | 1 | 88.6 | 1 | 89.1 | 1 | 82.1 | 1 | 87.6 | 1 |
| ACE2 | 90.8 | 1 | 90.8 | 1 | 90.8 | 1 | 68.6† | 1 | 90.8 | 7 | 68.8† | 4 | 52.0† | 1 | 43.5† | 1 |
| BAS1 | 91.1 | 1 | 91.1 | 1 | 92.8 | 1 | 91.1 | 1 | 92.8 | 2 | 83.7 | 3 | 88.3 | 1 | 70.6 | 10 |
| CBF1 | 80.6 | 1 | 79.2 | 1 | 79.2 | 1 | 84.8 | 1 | 85.5 | 1 | 81.6 | 1 | 83.9 | 1 | 81.2 | 1 |
| CIN5_H2O2Lo | 92.3 | 1 | 93.2 | 1 | 92.3 | 1 | 93.2 | 1 | 91.3 | 1 | 76.7 | 5 | 79.7 | 1 | 82.4 | 1 |
| DIG1 | 93.5 | 1 | 93.5 | 1 | 93.2 | 1 | 93.5 | 1 | 93.2 | 3 | 82.4 | 5 | 89.6 | 1 | 75.7 | 5 |
| FHL1* | 85.2 | 1 | 85.2 | 1 | 76.5 | 1 | 82.5 | 1 | 81.9 | 1 | 88.0 | 1 | 91.3 | 1 | 88.3 | 1 |
| FKH1 | 95.0 | 1 | 95.0 | 1 | 95.0 | 1 | 95.1 | 1 | 92.2 | 1 | 81.8 | 2 | 90.0 | 1 | 80.7 | 2 |
| FKH2 | 91.6 | 1 | 91.6 | 1 | 91.6 | 1 | 89.8 | 1 | 89.8 | 1 | 70.8 | 4 | 88.6 | 1 | 82.8 | 1 |
| GAL4_GAL* | 83.3 | 1 | 83.3 | 1 | 78.1 | 1 | 70.6 | 1 | 70.8 | 1 | 78.6 | 1 | 70.0 | 7 | 81.1 | 1 |
| HAP1* | 72.2 | 1 | 72.2 | 1 | 72.2 | 1 | 72.2 | 1 | 72.2 | 1 | 64.0† | 3 | 64.1† | 10 | 76.6 | 7 |
| HAP4 | 74.6 | 1 | 77.2 | 2 | 78.4 | 2 | 70.7 | 6 | 70.7 | 2 | 67.3† | 4 | 76.6 | 5 | 54.0† | 1 |
| HIR1* | 85.8 | 1 | 77.5 | 1 | 77.9 | 4 | 83.4 | 6 | 70.6 | 2 | 83.9 | 1 | 65.9† | 8 | 54.9† | 1 |
| HIR2* | 81.7 | 1 | 81.7 | 3 | 66.3† | 10 | 71.0 | 2 | 68.2† | 7 | 86.0 | 1 | 65.1† | 7 | 86.3 | 1 |
| MAC1_H2O2Hi | 79.3 | 1 | 79.3 | 1 | 86.9 | 1 | 85.2 | 2 | 85.5 | 2 | 81.6 | 2 | 73.2 | 1 | 68.1† | 1 |
| MBP1 | 92.9 | 1 | 92.6 | 1 | 91.9 | 1 | 90.6 | 1 | 88.7 | 1 | 83.5 | 3 | 86.0 | 1 | 67.1† | 3 |
| MCM1* | 79.7 | 1 | 78.0 | 1 | 78.9 | 1 | 77.0 | 1 | 77.8 | 1 | 75.1 | 1 | 76.2 | 1 | 70.9 | 1 |
| MET31 | 71.0 | 1 | 71.0 | 1 | 70.6 | 2 | 63.8† | 9 | 69.1† | 8 | 71.8 | 4 | 60.7† | 9 | 66.1† | 5 |
| MET32 | 76.2 | 3 | 76.6 | 2 | 72.4 | 3 | 70.3 | 7 | 70.3 | 10 | 64.3† | 4 | 52.7† | 9 | 57.3† | 4 |
| MET4 | 89.5 | 1 | 87.5 | 1 | 89.5 | 1 | 92.3 | 7 | 91.7 | 8 | 76.6 | 8 | 71.3 | 7 | 69.9† | 5 |
| MIG1 | 67.2† | 9 | 68.0† | 4 | 64.5† | 4 | 61.9† | 8 | 60.2† | 1 | 67.8† | 9 | 60.6† | 3 | 51.5† | 1 |
| MIG2 | 79.3 | 1 | 79.3 | 2 | 79.3 | 3 | 79.3 | 2 | 58.6† | 8 | 65.5† | 5 | 54.7† | 2 | 57.5† | 8 |
| MSN4_H2O2Hi | 84.6 | 3 | 77.4 | 3 | 74.6 | 3 | 74.3 | 4 | 74.6 | 1 | 70.1 | 6 | 61.0† | 8 | 66.3† | 8 |
| RAP1 | 79.6 | 1 | 74.3 | 1 | 78.8 | 1 | 73.1 | 1 | 82.4 | 1 | 83.6 | 1 | 81.6 | 1 | 80.2 | 1 |
| REB1 | 88.7 | 1 | 88.7 | 1 | 88.7 | 1 | 88.7 | 1 | 92.8 | 1 | 90.2 | 1 | 92.2 | 1 | 92.5 | 1 |
| RLM1* | 87.6 | 1 | 87.6 | 2 | 87.6 | 6 | 87.6 | 2 | 67.7† | 4 | 60.7† | 3 | 58.2† | 3 | 88.1 | 1 |
| SMP1* | 77.6 | 1 | 77.2 | 3 | 77.2 | 4 | 70.1 | 3 | 77.2 | 9 | 66.9† | 10 | 58.1† | 1 | 50.5† | 1 |
| STB1 | 81.8 | 1 | 75.8 | 2 | 79.7 | 1 | 75.8 | 3 | 71.3 | 1 | 80.1 | 2 | 74.7 | 1 | 79.2 | 1 |
| STE12 | 86.2 | 1 | 86.6 | 1 | 86.8 | 1 | 86.4 | 1 | 87.4 | 1 | 85.3 | 3 | 85.5 | 1 | 73.0 | 1 |
| SWI4 | 88.3 | 1 | 88.3 | 1 | 88.3 | 1 | 88.3 | 1 | 90.7 | 1 | 78.4 | 2 | 86.9 | 1 | 74.4 | 1 |
| SWI5 | 83.3 | 1 | 83.3 | 1 | 85.4 | 5 | 85.4 | 4 | 69.8† | 5 | 65.9† | 4 | 52.8† | 1 | 47.7† | 1 |
| TEC1 | 84.5 | 2 | 84.5 | 3 | 81.3 | 3 | 70.6 | 2 | 82.2 | 1 | 72.4 | 3 | 75.7 | 5 | 47.9† | 1 |
| Average | 83.9 | — | 83.0 | 82.4 | 80.5 | 79.9 | 76.3 | 73.4 | 70.4 | |||||||
| Top 1 pattern | 28 | 22 | 20 | 16 | 17 | 9 | 16 | 14 | ||||||||
| Top 2–5 patterns | 3 | 9 | 9 | 9 | 5 | 12 | 2 | 2 | ||||||||
| Top 6–10 patterns | 0 | 0 | 1 | 4 | 4 | 2 | 2 | 2 | ||||||||
| The correct motif not in top 10 | 1 | 1 | 2 | 3 | 6 | 9 | 12 | 14 | ||||||||
| No. gapped motifs identified | 9 | 9 | 8 | 9 | 7 | 6 | 4 | 7 | ||||||||
In our method, weights a (for position score) and b (for conservation score) in Eq. 4 are set at different values. Sim., similarity of the predicted motif to the annotated PFM.
*TFs with gapped motifs.
†Similarity scores (%)< 0.7 are considered failures.