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 ame_out --fix-partition 273 --bgformat 0 ./seqs-centered_w_bg db/JASPAR_CORE_2009.meme
Not in partition maximisation mode. Fixing partition at 273.
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 | MA0142.1 | Pou5f1 | top 273 seqs | 4.414e-20 | 2.101e-17 |
| 2. | Fisher-exact test | MA0143.1 | Sox2 | top 273 seqs | 1.351e-14 | 6.43e-12 |
| 3. | Fisher-exact test | MA00445.1 | D | top 273 seqs | 6.886e-11 | 3.278e-08 |
| 4. | Fisher-exact test | MA0077.1 | SOX9 | top 273 seqs | 1.577e-07 | 7.505e-05 |
| 5. | Fisher-exact test | MA0453.1 | nub | top 273 seqs | 1.733e-06 | 0.0008247 |