Table 2.
Results from motif discovery by MEME
| Full length regions |
Maximum ± 125 bp |
|||
|---|---|---|---|---|
| Best score | Top 5 | Best score | Top 5 | |
| Macs | 0 | 1 | 1 | 1 |
| Macs w background | 0 | 1 | 2 | 1 |
| SISSRs | 0 | 2 | 0 | 0 |
| SISSRs w background | 2 | 0 | 2 | 0 |
| FindPeaks w trim | 0 | 0 | 0 | 1 |
| PeakSeq | 1 | 1 | 1 | 1 |
| QuEST | – | – | 3 | 0 |
| Meta-approach | 3 | 0 | – | – |
| Manually evaluated | 3 | 0 | – | – |
Both full length regions and the regions created by adding/subtracting 125 bp around the maximum tag-intensity in each region were tested. The table shows the number of times the correct motif was identified as the best scoring one or was among the top five scoring motifs returned by MEME. Both in the meta-approach and the manually classified regions the correct motif was returned as the top scoring one for all three transcription factors.