If AME is of use to you in your research, please cite:
Robert McLeay and Timothy L. Bailey, "Motif Enrichment Analysis: A unified framework and method evaluation", BMC Bioinformatics, 11:165, 2010, doi:10.1186/1471-2105-11-165.
ame --verbose 1 --oc memechip_out/ame_out --fix-partition 820 --bgformat 0 memechip_out/seqs-centered_w_bg JASPAR_CORE_2009.meme
Not in partition maximisation mode. Fixing partition at 820.
Threshold p-value for reporting results: 0.001
Motif p-values are corrected by #Motifs × #ThresholdsTested – (476 × 1 = 476)
| motif number | scoring method | motif name | secondary motif name | scored sequences | p-value | corrected p-value |
|---|---|---|---|---|---|---|
| 1. | Fisher-exact test | MA0039.2 | Klf4 | top 820 seqs | 3.281e-63 | 1.562e-60 |
| 2. | Fisher-exact test | MA0140.1 | Tal1::Gata1 | top 820 seqs | 3.701e-28 | 1.761e-25 |
| 3. | Fisher-exact test | MA0035.2 | Gata1 | top 820 seqs | 3.701e-28 | 1.761e-25 |
| 4. | Fisher-exact test | MA0270.1 | AFT2 | top 820 seqs | 8.407e-23 | 4.002e-20 |
| 5. | Fisher-exact test | MA0300.1 | GAT1 | top 820 seqs | 3.02e-16 | 1.438e-13 |
| 6. | Fisher-exact test | MA0450.1 | hkb | top 820 seqs | 1.466e-13 | 6.976e-11 |
| 7. | Fisher-exact test | MA0443.1 | btd | top 820 seqs | 3.219e-11 | 1.532e-08 |
| 8. | Fisher-exact test | MA0309.1 | GZF3 | top 820 seqs | 7.745e-10 | 3.686e-07 |
| 9. | Fisher-exact test | MA0079.1 | SP1 | top 820 seqs | 6.103e-07 | 0.0002905 |