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 --oc results/mea_results_ame/Scl.ame_out --verbose 1 --fix-partition 2400 --bgformat 0 results/mea_results_ame/Scl-shuffled_w_bg.fa data/motif_databases/all_motifs.meme
Warning: Not in partition maximisation mode. Fixing partition at 2400.
Threshold p-value for reporting results: 0.001
Motif p-values are corrected by #Motifs × #ThresholdsTested – (863 × 1 = 863)
| motif number | scoring method | motif name | secondary motif name | scored sequences | p-value | corrected p-value |
|---|---|---|---|---|---|---|
| 1. | Fisher-exact p-value of motif | MA0140.1 | Tal1::Gata1 | top 2400 seqs | 4.199e-81 | 3.623e-78 |
| 2. | Fisher-exact p-value of motif | MA0035.2 | Gata1 | top 2400 seqs | 4.004e-49 | 3.455e-46 |
| 3. | Fisher-exact p-value of motif | Gata5_primary | top 2400 seqs | 8.063e-35 | 6.959e-32 | |
| 4. | Fisher-exact p-value of motif | Gata6_primary | top 2400 seqs | 2.234e-34 | 1.928e-31 | |
| 5. | Fisher-exact p-value of motif | Gata3_primary | top 2400 seqs | 1.733e-31 | 1.495e-28 | |
| 6. | Fisher-exact p-value of motif | MA0300.1 | GAT1 | top 2400 seqs | 1.434e-29 | 1.238e-26 |
| 7. | Fisher-exact p-value of motif | Klf7_primary | top 2400 seqs | 2.094e-23 | 1.807e-20 | |
| 8. | Fisher-exact p-value of motif | MA0149.1 | EWSR1-FLI1 | top 2400 seqs | 6.444e-20 | 5.561e-17 |
| 9. | Fisher-exact p-value of motif | MA0309.1 | GZF3 | top 2400 seqs | 7.584e-20 | 6.545e-17 |
| 10. | Fisher-exact p-value of motif | Zfp410_secondary | top 2400 seqs | 8.119e-19 | 7.007e-16 | |
| 11. | Fisher-exact p-value of motif | Elf3_primary | top 2400 seqs | 1.508e-18 | 1.301e-15 | |
| 12. | Fisher-exact p-value of motif | MA0039.2 | Klf4 | top 2400 seqs | 9.182e-17 | 7.924e-14 |
| 13. | Fisher-exact p-value of motif | MA0443.1 | btd | top 2400 seqs | 1.578e-15 | 1.362e-12 |
| 14. | Fisher-exact p-value of motif | Sp4_primary | top 2400 seqs | 2.699e-15 | 2.33e-12 | |
| 15. | Fisher-exact p-value of motif | MA0162.1 | Egr1 | top 2400 seqs | 3.233e-15 | 2.79e-12 |
| 16. | Fisher-exact p-value of motif | MA0450.1 | hkb | top 2400 seqs | 8.395e-15 | 7.245e-12 |
| 17. | Fisher-exact p-value of motif | Ascl2_secondary | top 2400 seqs | 2.046e-14 | 1.765e-11 | |
| 18. | Fisher-exact p-value of motif | Zfp281_secondary | top 2400 seqs | 2.568e-14 | 2.216e-11 | |
| 19. | Fisher-exact p-value of motif | MA0399.1 | SUT1 | top 2400 seqs | 3.188e-14 | 2.751e-11 |
| 20. | Fisher-exact p-value of motif | MA0062.2 | GABPA | top 2400 seqs | 3.343e-14 | 2.885e-11 |
| 21. | Fisher-exact p-value of motif | Smad3_secondary | top 2400 seqs | 5.75e-14 | 4.962e-11 | |
| 22. | Fisher-exact p-value of motif | Gabpa_secondary | top 2400 seqs | 1.076e-13 | 9.284e-11 | |
| 23. | Fisher-exact p-value of motif | Bcl6b_secondary | top 2400 seqs | 2.306e-13 | 1.99e-10 | |
| 24. | Fisher-exact p-value of motif | MA0079.2 | SP1 | top 2400 seqs | 8.482e-13 | 7.32e-10 |
| 25. | Fisher-exact p-value of motif | MA0333.1 | MET31 | top 2400 seqs | 3.308e-12 | 2.855e-09 |
| 26. | Fisher-exact p-value of motif | MA0283.1 | CHA4 | top 2400 seqs | 3.975e-12 | 3.43e-09 |
| 27. | Fisher-exact p-value of motif | MA0334.1 | MET32 | top 2400 seqs | 1.209e-11 | 1.044e-08 |
| 28. | Fisher-exact p-value of motif | MA0073.1 | RREB1 | top 2400 seqs | 1.907e-11 | 1.646e-08 |
| 29. | Fisher-exact p-value of motif | MA0080.2 | SPI1 | top 2400 seqs | 3.284e-11 | 2.834e-08 |
| 30. | Fisher-exact p-value of motif | MA0410.1 | UGA3 | top 2400 seqs | 2.68e-10 | 2.313e-07 |
| 31. | Fisher-exact p-value of motif | MA0374.1 | RSC3 | top 2400 seqs | 3.358e-10 | 2.898e-07 |
| 32. | Fisher-exact p-value of motif | Zbtb7b_primary | top 2400 seqs | 3.937e-10 | 3.398e-07 | |
| 33. | Fisher-exact p-value of motif | MA0156.1 | FEV | top 2400 seqs | 4.414e-10 | 3.809e-07 |
| 34. | Fisher-exact p-value of motif | MA0045.1 | HMG-I/Y | top 2400 seqs | 5.824e-10 | 5.026e-07 |
| 35. | Fisher-exact p-value of motif | MA0285.1 | CRZ1 | top 2400 seqs | 9.547e-10 | 8.239e-07 |
| 36. | Fisher-exact p-value of motif | Zfp281_primary | top 2400 seqs | 1.234e-09 | 1.065e-06 | |
| 37. | Fisher-exact p-value of motif | Mtf1_secondary | top 2400 seqs | 1.636e-09 | 1.412e-06 | |
| 38. | Fisher-exact p-value of motif | MA0395.1 | STP2 | top 2400 seqs | 2.067e-09 | 1.784e-06 |
| 39. | Fisher-exact p-value of motif | MA0449.1 | h | top 2400 seqs | 2.34e-09 | 2.019e-06 |
| 40. | Fisher-exact p-value of motif | MA0062.1 | GABPA | top 2400 seqs | 2.734e-09 | 2.359e-06 |
| 41. | Fisher-exact p-value of motif | Foxl1_primary | top 2400 seqs | 3.242e-09 | 2.798e-06 | |
| 42. | Fisher-exact p-value of motif | Ehf_primary | top 2400 seqs | 3.337e-09 | 2.879e-06 | |
| 43. | Fisher-exact p-value of motif | MA0375.1 | RSC30 | top 2400 seqs | 4.511e-09 | 3.893e-06 |
| 44. | Fisher-exact p-value of motif | MA0157.1 | FOXO3 | top 2400 seqs | 9.325e-09 | 8.048e-06 |
| 45. | Fisher-exact p-value of motif | MA0137.1 | STAT1 | top 2400 seqs | 1.173e-08 | 1.012e-05 |
| 46. | Fisher-exact p-value of motif | MA0026.1 | Eip74EF | top 2400 seqs | 1.226e-08 | 1.058e-05 |
| 47. | Fisher-exact p-value of motif | Srf_secondary | top 2400 seqs | 1.243e-08 | 1.072e-05 | |
| 48. | Fisher-exact p-value of motif | SCGCMGC | top 2400 seqs | 1.351e-08 | 1.166e-05 | |
| 49. | Fisher-exact p-value of motif | MA0408.1 | TOS8 | top 2400 seqs | 1.574e-08 | 1.358e-05 |
| 50. | Fisher-exact p-value of motif | MA0136.1 | ELF5 | top 2400 seqs | 1.607e-08 | 1.387e-05 |
| 51. | Fisher-exact p-value of motif | Gm397_secondary | top 2400 seqs | 2.361e-08 | 2.038e-05 | |
| 52. | Fisher-exact p-value of motif | MA0042.1 | FOXI1 | top 2400 seqs | 2.643e-08 | 2.281e-05 |
| 53. | Fisher-exact p-value of motif | Zfp740_secondary | top 2400 seqs | 2.691e-08 | 2.322e-05 | |
| 54. | Fisher-exact p-value of motif | Zfp161_primary | top 2400 seqs | 2.743e-08 | 2.368e-05 | |
| 55. | Fisher-exact p-value of motif | MA0361.1 | RDS1 | top 2400 seqs | 3.849e-08 | 3.321e-05 |
| 56. | Fisher-exact p-value of motif | Nkx2-2_2823.1 | top 2400 seqs | 4.941e-08 | 4.264e-05 | |
| 57. | Fisher-exact p-value of motif | Glis2_primary | top 2400 seqs | 5.427e-08 | 4.683e-05 | |
| 58. | Fisher-exact p-value of motif | Nkx2-5_3436.1 | top 2400 seqs | 6.252e-08 | 5.395e-05 | |
| 59. | Fisher-exact p-value of motif | MA0394.1 | STP1 | top 2400 seqs | 7.619e-08 | 6.575e-05 |
| 60. | Fisher-exact p-value of motif | MA0277.1 | AZF1 | top 2400 seqs | 9.117e-08 | 7.868e-05 |
| 61. | Fisher-exact p-value of motif | Egr1_primary | top 2400 seqs | 1.154e-07 | 9.958e-05 | |
| 62. | Fisher-exact p-value of motif | Myf6_secondary | top 2400 seqs | 1.171e-07 | 0.000101 | |
| 63. | Fisher-exact p-value of motif | MA0030.1 | FOXF2 | top 2400 seqs | 1.607e-07 | 0.0001387 |
| 64. | Fisher-exact p-value of motif | MA0079.1 | SP1 | top 2400 seqs | 1.663e-07 | 0.0001435 |
| 65. | Fisher-exact p-value of motif | MA0297.1 | FKH2 | top 2400 seqs | 2.372e-07 | 0.0002046 |
| 66. | Fisher-exact p-value of motif | MA0029.1 | Evi1 | top 2400 seqs | 4.94e-07 | 0.0004262 |
| 67. | Fisher-exact p-value of motif | Titf1_1722.2 | top 2400 seqs | 5.464e-07 | 0.0004714 | |
| 68. | Fisher-exact p-value of motif | MA0332.1 | MET28 | top 2400 seqs | 5.513e-07 | 0.0004757 |
| 69. | Fisher-exact p-value of motif | MA0458.1 | slp1 | top 2400 seqs | 6.626e-07 | 0.0005717 |
| 70. | Fisher-exact p-value of motif | MA0096.1 | bZIP910 | top 2400 seqs | 7.094e-07 | 0.000612 |