AME (Analysis of Motif Enrichment): Compiled on Mar 2 2012 at 16:08:25 ------------------------------ Copyright (c) Robert McLeay & Timothy Bailey , 2009. Command line ame --oc results/mea_results_ame/Smad1.ame_out --verbose 1 --fix-partition 1126 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_Smad1_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme Not in partition maximisation mode. Fixing partition at 1126. Threshold p-value for reporting results: 0.001 Motif p-values are corrected by #Motifs * #ThresholdsTested - (532 * 1 = 532) 1. Fisher-exact p-value of motif MA0142.1 Pou5f1 top 1126 seqs: 1.088e-58 (Corrected p-value: 5.788e-56) 2. Fisher-exact p-value of motif MA0143.1 Sox2 top 1126 seqs: 3.322e-47 (Corrected p-value: 1.767e-44) 3. Fisher-exact p-value of motif MA0039.2 Klf4 top 1126 seqs: 1.99e-28 (Corrected p-value: 1.059e-25) 4. Fisher-exact p-value of motif UP00062_1 Sox4_primary top 1126 seqs: 1.99e-26 (Corrected p-value: 1.058e-23) 5. Fisher-exact p-value of motif UP00030_1 Sox11_primary top 1126 seqs: 3.187e-26 (Corrected p-value: 1.696e-23) 6. Fisher-exact p-value of motif UP00191_1 Pou2f2_3748.1 top 1126 seqs: 4.43e-24 (Corrected p-value: 2.357e-21) 7. Fisher-exact p-value of motif UP00179_1 Pou2f3_3986.2 top 1126 seqs: 4.43e-24 (Corrected p-value: 2.357e-21) 8. Fisher-exact p-value of motif UP00093_1 Klf7_primary top 1126 seqs: 1.209e-21 (Corrected p-value: 6.432e-19) 9. Fisher-exact p-value of motif MA0079.2 SP1 top 1126 seqs: 5.412e-21 (Corrected p-value: 2.879e-18) 10. Fisher-exact p-value of motif UP00102_2 Zic1_secondary top 1126 seqs: 3.866e-19 (Corrected p-value: 2.057e-16) 11. Fisher-exact p-value of motif UP00006_2 Zic3_secondary top 1126 seqs: 4.724e-19 (Corrected p-value: 2.513e-16) 12. Fisher-exact p-value of motif UP00057_2 Zic2_secondary top 1126 seqs: 5.71e-19 (Corrected p-value: 3.038e-16) 13. Fisher-exact p-value of motif UP00099_2 Ascl2_secondary top 1126 seqs: 8.863e-18 (Corrected p-value: 4.715e-15) 14. Fisher-exact p-value of motif UP00021_1 Zfp281_primary top 1126 seqs: 8.99e-18 (Corrected p-value: 4.783e-15) 15. Fisher-exact p-value of motif UP00034_1 Sox7_primary top 1126 seqs: 3.904e-17 (Corrected p-value: 2.077e-14) 16. Fisher-exact p-value of motif UP00023_1 Sox30_primary top 1126 seqs: 1.032e-16 (Corrected p-value: 5.488e-14) 17. Fisher-exact p-value of motif UP00002_1 Sp4_primary top 1126 seqs: 7.26e-16 (Corrected p-value: 3.862e-13) 18. Fisher-exact p-value of motif UP00043_2 Bcl6b_secondary top 1126 seqs: 1.378e-15 (Corrected p-value: 7.331e-13) 19. Fisher-exact p-value of motif MA0073.1 RREB1 top 1126 seqs: 1.684e-15 (Corrected p-value: 8.961e-13) 20. Fisher-exact p-value of motif UP00061_1 Foxl1_primary top 1126 seqs: 1.567e-14 (Corrected p-value: 8.335e-12) 21. Fisher-exact p-value of motif UP00101_2 Sox12_secondary top 1126 seqs: 7.403e-14 (Corrected p-value: 3.938e-11) 22. Fisher-exact p-value of motif UP00101_1 Sox12_primary top 1126 seqs: 1.017e-13 (Corrected p-value: 5.413e-11) 23. Fisher-exact p-value of motif UP00004_2 Sox14_secondary top 1126 seqs: 3.885e-13 (Corrected p-value: 2.067e-10) 24. Fisher-exact p-value of motif MA0162.1 Egr1 top 1126 seqs: 8.149e-13 (Corrected p-value: 4.335e-10) 25. Fisher-exact p-value of motif MA0084.1 SRY top 1126 seqs: 1.291e-12 (Corrected p-value: 6.868e-10) 26. Fisher-exact p-value of motif UP00033_2 Zfp410_secondary top 1126 seqs: 1.622e-12 (Corrected p-value: 8.627e-10) 27. Fisher-exact p-value of motif MA0079.1 SP1 top 1126 seqs: 7.198e-12 (Corrected p-value: 3.829e-09) 28. Fisher-exact p-value of motif UP00000_2 Smad3_secondary top 1126 seqs: 1.992e-11 (Corrected p-value: 1.06e-08) 29. Fisher-exact p-value of motif MA0062.1 GABPA top 1126 seqs: 2.117e-11 (Corrected p-value: 1.126e-08) 30. Fisher-exact p-value of motif UP00211_1 Pou3f3_3235.2 top 1126 seqs: 2.528e-11 (Corrected p-value: 1.345e-08) 31. Fisher-exact p-value of motif MA0077.1 SOX9 top 1126 seqs: 3.384e-11 (Corrected p-value: 1.801e-08) 32. Fisher-exact p-value of motif UP00021_2 Zfp281_secondary top 1126 seqs: 4.728e-11 (Corrected p-value: 2.515e-08) 33. Fisher-exact p-value of motif UP00096_2 Sox13_secondary top 1126 seqs: 2.465e-10 (Corrected p-value: 1.311e-07) 34. Fisher-exact p-value of motif UP00061_2 Foxl1_secondary top 1126 seqs: 2.896e-10 (Corrected p-value: 1.541e-07) 35. Fisher-exact p-value of motif UP00097_2 Mtf1_secondary top 1126 seqs: 3.045e-10 (Corrected p-value: 1.62e-07) 36. Fisher-exact p-value of motif UP00408_2 Gabpa_secondary top 1126 seqs: 5.247e-10 (Corrected p-value: 2.791e-07) 37. Fisher-exact p-value of motif UP00047_1 Zbtb7b_primary top 1126 seqs: 5.27e-10 (Corrected p-value: 2.804e-07) 38. Fisher-exact p-value of motif MA0078.1 Sox17 top 1126 seqs: 5.714e-10 (Corrected p-value: 3.04e-07) 39. Fisher-exact p-value of motif MA0042.1 FOXI1 top 1126 seqs: 7.271e-10 (Corrected p-value: 3.868e-07) 40. Fisher-exact p-value of motif UP00099_1 Ascl2_primary top 1126 seqs: 1.459e-09 (Corrected p-value: 7.76e-07) 41. Fisher-exact p-value of motif MA0149.1 EWSR1-FLI1 top 1126 seqs: 1.933e-09 (Corrected p-value: 1.029e-06) 42. Fisher-exact p-value of motif UP00073_1 Foxa2_primary top 1126 seqs: 2.066e-09 (Corrected p-value: 1.099e-06) 43. Fisher-exact p-value of motif UP00042_2 Gm397_secondary top 1126 seqs: 5.593e-09 (Corrected p-value: 2.975e-06) 44. Fisher-exact p-value of motif MA0060.1 NFYA top 1126 seqs: 2.039e-08 (Corrected p-value: 1.085e-05) 45. Fisher-exact p-value of motif UP00037_1 Zfp105_primary top 1126 seqs: 2.073e-08 (Corrected p-value: 1.103e-05) 46. Fisher-exact p-value of motif MA0030.1 FOXF2 top 1126 seqs: 3.078e-08 (Corrected p-value: 1.638e-05) 47. Fisher-exact p-value of motif UP00075_1 Sox15_primary top 1126 seqs: 3.231e-08 (Corrected p-value: 1.719e-05) 48. Fisher-exact p-value of motif UP00046_1 Tcfe2a_primary top 1126 seqs: 3.242e-08 (Corrected p-value: 1.725e-05) 49. Fisher-exact p-value of motif UP00025_1 Foxk1_primary top 1126 seqs: 3.489e-08 (Corrected p-value: 1.856e-05) 50. Fisher-exact p-value of motif UP00079_1 Esrra_primary top 1126 seqs: 3.532e-08 (Corrected p-value: 1.879e-05) 51. Fisher-exact p-value of motif UP00016_2 Sry_secondary top 1126 seqs: 3.729e-08 (Corrected p-value: 1.984e-05) 52. Fisher-exact p-value of motif UP00041_1 Foxj1_primary top 1126 seqs: 4.365e-08 (Corrected p-value: 2.322e-05) 53. Fisher-exact p-value of motif UP00408_1 Gabpa_primary top 1126 seqs: 4.366e-08 (Corrected p-value: 2.323e-05) 54. Fisher-exact p-value of motif MA0062.2 GABPA top 1126 seqs: 4.99e-08 (Corrected p-value: 2.655e-05) 55. Fisher-exact p-value of motif MA0039.1 Klf4 top 1126 seqs: 6.63e-08 (Corrected p-value: 3.527e-05) 56. Fisher-exact p-value of motif UP00064_1 Sox18_primary top 1126 seqs: 7.436e-08 (Corrected p-value: 3.956e-05) 57. Fisher-exact p-value of motif MA0004.1 Arnt top 1126 seqs: 7.562e-08 (Corrected p-value: 4.023e-05) 58. Fisher-exact p-value of motif MA0093.1 USF1 top 1126 seqs: 7.562e-08 (Corrected p-value: 4.023e-05) 59. Fisher-exact p-value of motif MA0104.1 Mycn top 1126 seqs: 7.562e-08 (Corrected p-value: 4.023e-05) 60. Fisher-exact p-value of motif UP00255_1 Dbx1_3486.1 top 1126 seqs: 1.088e-07 (Corrected p-value: 5.786e-05) 61. Fisher-exact p-value of motif MA0144.1 Stat3 top 1126 seqs: 1.362e-07 (Corrected p-value: 7.243e-05) 62. Fisher-exact p-value of motif UP00022_1 Zfp740_primary top 1126 seqs: 1.43e-07 (Corrected p-value: 7.607e-05) 63. Fisher-exact p-value of motif UP00039_1 Foxj3_primary top 1126 seqs: 1.915e-07 (Corrected p-value: 0.0001019) 64. Fisher-exact p-value of motif MA0141.1 Esrrb top 1126 seqs: 2.092e-07 (Corrected p-value: 0.0001113) 65. Fisher-exact p-value of motif MA0137.2 STAT1 top 1126 seqs: 2.626e-07 (Corrected p-value: 0.0001397) 66. Fisher-exact p-value of motif MA0069.1 Pax6 top 1126 seqs: 3.363e-07 (Corrected p-value: 0.0001789)