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/STAT3.ame_out --verbose 1 --fix-partition 2546 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_STAT3_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme Not in partition maximisation mode. Fixing partition at 2546. 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 MA0137.2 STAT1 top 2546 seqs: 1.259e-122 (Corrected p-value: 6.697e-120) 2. Fisher-exact p-value of motif MA0144.1 Stat3 top 2546 seqs: 1.205e-108 (Corrected p-value: 6.41e-106) 3. Fisher-exact p-value of motif MA0039.2 Klf4 top 2546 seqs: 3.278e-63 (Corrected p-value: 1.744e-60) 4. Fisher-exact p-value of motif UP00093_1 Klf7_primary top 2546 seqs: 3.256e-58 (Corrected p-value: 1.732e-55) 5. Fisher-exact p-value of motif UP00002_1 Sp4_primary top 2546 seqs: 1.152e-40 (Corrected p-value: 6.127e-38) 6. Fisher-exact p-value of motif UP00099_2 Ascl2_secondary top 2546 seqs: 7.199e-40 (Corrected p-value: 3.83e-37) 7. Fisher-exact p-value of motif UP00021_2 Zfp281_secondary top 2546 seqs: 3.576e-39 (Corrected p-value: 1.903e-36) 8. Fisher-exact p-value of motif MA0073.1 RREB1 top 2546 seqs: 5.488e-35 (Corrected p-value: 2.92e-32) 9. Fisher-exact p-value of motif MA0149.1 EWSR1-FLI1 top 2546 seqs: 2.735e-34 (Corrected p-value: 1.455e-31) 10. Fisher-exact p-value of motif MA0142.1 Pou5f1 top 2546 seqs: 2.653e-33 (Corrected p-value: 1.411e-30) 11. Fisher-exact p-value of motif MA0079.2 SP1 top 2546 seqs: 7.49e-31 (Corrected p-value: 3.985e-28) 12. Fisher-exact p-value of motif UP00047_1 Zbtb7b_primary top 2546 seqs: 1.767e-30 (Corrected p-value: 9.399e-28) 13. Fisher-exact p-value of motif UP00000_2 Smad3_secondary top 2546 seqs: 5.719e-30 (Corrected p-value: 3.043e-27) 14. Fisher-exact p-value of motif MA0143.1 Sox2 top 2546 seqs: 1.358e-29 (Corrected p-value: 7.227e-27) 15. Fisher-exact p-value of motif MA0062.2 GABPA top 2546 seqs: 1.823e-29 (Corrected p-value: 9.699e-27) 16. Fisher-exact p-value of motif UP00021_1 Zfp281_primary top 2546 seqs: 6.67e-29 (Corrected p-value: 3.548e-26) 17. Fisher-exact p-value of motif UP00022_2 Zfp740_secondary top 2546 seqs: 9.212e-29 (Corrected p-value: 4.901e-26) 18. Fisher-exact p-value of motif MA0162.1 Egr1 top 2546 seqs: 3.273e-28 (Corrected p-value: 1.741e-25) 19. Fisher-exact p-value of motif UP00015_1 Ehf_primary top 2546 seqs: 3.404e-28 (Corrected p-value: 1.811e-25) 20. Fisher-exact p-value of motif UP00407_1 Elf3_primary top 2546 seqs: 7.3e-28 (Corrected p-value: 3.884e-25) 21. Fisher-exact p-value of motif UP00033_2 Zfp410_secondary top 2546 seqs: 1.191e-27 (Corrected p-value: 6.338e-25) 22. Fisher-exact p-value of motif MA0156.1 FEV top 2546 seqs: 3.166e-26 (Corrected p-value: 1.685e-23) 23. Fisher-exact p-value of motif UP00043_2 Bcl6b_secondary top 2546 seqs: 1.3e-25 (Corrected p-value: 6.914e-23) 24. Fisher-exact p-value of motif UP00408_2 Gabpa_secondary top 2546 seqs: 5.451e-24 (Corrected p-value: 2.9e-21) 25. Fisher-exact p-value of motif UP00024_1 Glis2_primary top 2546 seqs: 9.567e-24 (Corrected p-value: 5.089e-21) 26. Fisher-exact p-value of motif UP00062_1 Sox4_primary top 2546 seqs: 5.615e-23 (Corrected p-value: 2.987e-20) 27. Fisher-exact p-value of motif UP00191_1 Pou2f2_3748.1 top 2546 seqs: 7.356e-22 (Corrected p-value: 3.913e-19) 28. Fisher-exact p-value of motif MA0068.1 Pax4 top 2546 seqs: 1.622e-21 (Corrected p-value: 8.63e-19) 29. Fisher-exact p-value of motif UP00030_1 Sox11_primary top 2546 seqs: 2.37e-21 (Corrected p-value: 1.261e-18) 30. Fisher-exact p-value of motif UP00007_1 Egr1_primary top 2546 seqs: 7.388e-21 (Corrected p-value: 3.93e-18) 31. Fisher-exact p-value of motif UP00073_1 Foxa2_primary top 2546 seqs: 2.558e-19 (Corrected p-value: 1.361e-16) 32. Fisher-exact p-value of motif UP00179_1 Pou2f3_3986.2 top 2546 seqs: 4.472e-19 (Corrected p-value: 2.379e-16) 33. Fisher-exact p-value of motif MA0079.1 SP1 top 2546 seqs: 1.111e-18 (Corrected p-value: 5.91e-16) 34. Fisher-exact p-value of motif MA0062.1 GABPA top 2546 seqs: 2.425e-18 (Corrected p-value: 1.29e-15) 35. Fisher-exact p-value of motif UP00025_1 Foxk1_primary top 2546 seqs: 2.713e-18 (Corrected p-value: 1.443e-15) 36. Fisher-exact p-value of motif MA0039.1 Klf4 top 2546 seqs: 3.807e-17 (Corrected p-value: 2.025e-14) 37. Fisher-exact p-value of motif UP00061_1 Foxl1_primary top 2546 seqs: 4.223e-17 (Corrected p-value: 2.247e-14) 38. Fisher-exact p-value of motif UP00043_1 Bcl6b_primary top 2546 seqs: 2.106e-16 (Corrected p-value: 1.12e-13) 39. Fisher-exact p-value of motif UP00408_1 Gabpa_primary top 2546 seqs: 6.624e-16 (Corrected p-value: 3.524e-13) 40. Fisher-exact p-value of motif MA0041.1 Foxd3 top 2546 seqs: 8.798e-16 (Corrected p-value: 4.681e-13) 41. Fisher-exact p-value of motif UP00077_2 Srf_secondary top 2546 seqs: 1.461e-15 (Corrected p-value: 7.77e-13) 42. Fisher-exact p-value of motif UP00101_2 Sox12_secondary top 2546 seqs: 2.354e-15 (Corrected p-value: 1.252e-12) 43. Fisher-exact p-value of motif MA0136.1 ELF5 top 2546 seqs: 3.109e-15 (Corrected p-value: 1.654e-12) 44. Fisher-exact p-value of motif UP00061_2 Foxl1_secondary top 2546 seqs: 3.141e-15 (Corrected p-value: 1.671e-12) 45. Fisher-exact p-value of motif MA0076.1 ELK4 top 2546 seqs: 8.879e-15 (Corrected p-value: 4.724e-12) 46. Fisher-exact p-value of motif UP00088_2 Plagl1_secondary top 2546 seqs: 1.202e-14 (Corrected p-value: 6.397e-12) 47. Fisher-exact p-value of motif UP00022_1 Zfp740_primary top 2546 seqs: 2.594e-14 (Corrected p-value: 1.38e-11) 48. Fisher-exact p-value of motif MA0157.1 FOXO3 top 2546 seqs: 3.959e-14 (Corrected p-value: 2.106e-11) 49. Fisher-exact p-value of motif MA0137.1 STAT1 top 2546 seqs: 6.329e-14 (Corrected p-value: 3.367e-11) 50. Fisher-exact p-value of motif UP00097_2 Mtf1_secondary top 2546 seqs: 6.945e-14 (Corrected p-value: 3.695e-11) 51. Fisher-exact p-value of motif UP00039_1 Foxj3_primary top 2546 seqs: 8.017e-14 (Corrected p-value: 4.265e-11) 52. Fisher-exact p-value of motif UP00041_1 Foxj1_primary top 2546 seqs: 1.285e-13 (Corrected p-value: 6.839e-11) 53. Fisher-exact p-value of motif UP00073_2 Foxa2_secondary top 2546 seqs: 2.521e-13 (Corrected p-value: 1.341e-10) 54. Fisher-exact p-value of motif UP00029_1 Tbp_primary top 2546 seqs: 2.666e-13 (Corrected p-value: 1.418e-10) 55. Fisher-exact p-value of motif MA0047.2 Foxa2 top 2546 seqs: 3.283e-13 (Corrected p-value: 1.747e-10) 56. Fisher-exact p-value of motif UP00088_1 Plagl1_primary top 2546 seqs: 4.232e-13 (Corrected p-value: 2.251e-10) 57. Fisher-exact p-value of motif MA0004.1 Arnt top 2546 seqs: 5.15e-13 (Corrected p-value: 2.74e-10) 58. Fisher-exact p-value of motif MA0104.1 Mycn top 2546 seqs: 5.15e-13 (Corrected p-value: 2.74e-10) 59. Fisher-exact p-value of motif MA0093.1 USF1 top 2546 seqs: 5.15e-13 (Corrected p-value: 2.74e-10) 60. Fisher-exact p-value of motif UP00096_2 Sox13_secondary top 2546 seqs: 5.936e-13 (Corrected p-value: 3.158e-10) 61. Fisher-exact p-value of motif UP00406_1 Spdef_primary top 2546 seqs: 7.474e-13 (Corrected p-value: 3.976e-10) 62. Fisher-exact p-value of motif MA0084.1 SRY top 2546 seqs: 1.301e-12 (Corrected p-value: 6.924e-10) 63. Fisher-exact p-value of motif MA0141.1 Esrrb top 2546 seqs: 1.575e-12 (Corrected p-value: 8.378e-10) 64. Fisher-exact p-value of motif UP00057_2 Zic2_secondary top 2546 seqs: 3.504e-12 (Corrected p-value: 1.864e-09) 65. Fisher-exact p-value of motif MA0148.1 FOXA1 top 2546 seqs: 3.624e-12 (Corrected p-value: 1.928e-09) 66. Fisher-exact p-value of motif UP00006_2 Zic3_secondary top 2546 seqs: 3.665e-12 (Corrected p-value: 1.95e-09) 67. Fisher-exact p-value of motif UP00034_1 Sox7_primary top 2546 seqs: 9.474e-12 (Corrected p-value: 5.04e-09) 68. Fisher-exact p-value of motif UP00037_1 Zfp105_primary top 2546 seqs: 5.101e-11 (Corrected p-value: 2.714e-08) 69. Fisher-exact p-value of motif UP00086_1 Irf3_primary top 2546 seqs: 7.318e-11 (Corrected p-value: 3.893e-08) 70. Fisher-exact p-value of motif MA0105.1 NFKB1 top 2546 seqs: 8.496e-11 (Corrected p-value: 4.52e-08) 71. Fisher-exact p-value of motif MA0050.1 IRF1 top 2546 seqs: 9.508e-11 (Corrected p-value: 5.058e-08) 72. Fisher-exact p-value of motif MA0080.2 SPI1 top 2546 seqs: 1.095e-10 (Corrected p-value: 5.825e-08) 73. Fisher-exact p-value of motif MA0030.1 FOXF2 top 2546 seqs: 1.987e-10 (Corrected p-value: 1.057e-07) 74. Fisher-exact p-value of motif UP00102_2 Zic1_secondary top 2546 seqs: 2.43e-10 (Corrected p-value: 1.293e-07) 75. Fisher-exact p-value of motif UP00035_2 Hic1_secondary top 2546 seqs: 2.927e-10 (Corrected p-value: 1.557e-07) 76. Fisher-exact p-value of motif MA0160.1 NR4A2 top 2546 seqs: 3.613e-10 (Corrected p-value: 1.922e-07) 77. Fisher-exact p-value of motif MA0042.1 FOXI1 top 2546 seqs: 5.517e-10 (Corrected p-value: 2.935e-07) 78. Fisher-exact p-value of motif UP00047_2 Zbtb7b_secondary top 2546 seqs: 1.447e-09 (Corrected p-value: 7.697e-07) 79. Fisher-exact p-value of motif MA0088.1 znf143 top 2546 seqs: 1.659e-09 (Corrected p-value: 8.825e-07) 80. Fisher-exact p-value of motif UP00074_1 Isgf3g_primary top 2546 seqs: 4.242e-09 (Corrected p-value: 2.257e-06) 81. Fisher-exact p-value of motif MA0058.1 MAX top 2546 seqs: 4.983e-09 (Corrected p-value: 2.651e-06) 82. Fisher-exact p-value of motif UP00042_2 Gm397_secondary top 2546 seqs: 5.124e-09 (Corrected p-value: 2.726e-06) 83. Fisher-exact p-value of motif MA0164.1 Nr2e3 top 2546 seqs: 5.578e-09 (Corrected p-value: 2.968e-06) 84. Fisher-exact p-value of motif UP00227_1 Duxl_1286.2 top 2546 seqs: 8.135e-09 (Corrected p-value: 4.328e-06) 85. Fisher-exact p-value of motif MA0055.1 Myf top 2546 seqs: 9.243e-09 (Corrected p-value: 4.917e-06) 86. Fisher-exact p-value of motif UP00075_1 Sox15_primary top 2546 seqs: 9.832e-09 (Corrected p-value: 5.231e-06) 87. Fisher-exact p-value of motif UP00101_1 Sox12_primary top 2546 seqs: 1.129e-08 (Corrected p-value: 6.006e-06) 88. Fisher-exact p-value of motif MA0116.1 Zfp423 top 2546 seqs: 1.305e-08 (Corrected p-value: 6.945e-06) 89. Fisher-exact p-value of motif UP00051_1 Sox8_primary top 2546 seqs: 1.427e-08 (Corrected p-value: 7.593e-06) 90. Fisher-exact p-value of motif UP00094_2 Zfp128_secondary top 2546 seqs: 4.011e-08 (Corrected p-value: 2.134e-05) 91. Fisher-exact p-value of motif UP00099_1 Ascl2_primary top 2546 seqs: 4.299e-08 (Corrected p-value: 2.287e-05) 92. Fisher-exact p-value of motif UP00255_1 Dbx1_3486.1 top 2546 seqs: 8.634e-08 (Corrected p-value: 4.593e-05) 93. Fisher-exact p-value of motif MA0048.1 NHLH1 top 2546 seqs: 8.739e-08 (Corrected p-value: 4.649e-05) 94. Fisher-exact p-value of motif UP00050_1 Bhlhb2_primary top 2546 seqs: 2.232e-07 (Corrected p-value: 0.0001187) 95. Fisher-exact p-value of motif UP00244_1 Tlx2_3498.2 top 2546 seqs: 2.988e-07 (Corrected p-value: 0.000159) 96. Fisher-exact p-value of motif UP00054_2 Tcf7_secondary top 2546 seqs: 3.622e-07 (Corrected p-value: 0.0001927) 97. Fisher-exact p-value of motif UP00035_1 Hic1_primary top 2546 seqs: 4.97e-07 (Corrected p-value: 0.0002644) 98. Fisher-exact p-value of motif UP00079_1 Esrra_primary top 2546 seqs: 6.224e-07 (Corrected p-value: 0.000331) 99. Fisher-exact p-value of motif MA0040.1 Foxq1 top 2546 seqs: 7.394e-07 (Corrected p-value: 0.0003933) 100. Fisher-exact p-value of motif MA0052.1 MEF2A top 2546 seqs: 9.66e-07 (Corrected p-value: 0.0005138) 101. Fisher-exact p-value of motif MA0077.1 SOX9 top 2546 seqs: 1.136e-06 (Corrected p-value: 0.000604) 102. Fisher-exact p-value of motif MA0102.2 CEBPA top 2546 seqs: 1.157e-06 (Corrected p-value: 0.0006156) 103. Fisher-exact p-value of motif UP00217_1 Hoxa10_2318.1 top 2546 seqs: 1.186e-06 (Corrected p-value: 0.0006308) 104. Fisher-exact p-value of motif UP00231_1 Nkx2-2_2823.1 top 2546 seqs: 1.58e-06 (Corrected p-value: 0.0008402) 105. Fisher-exact p-value of motif MA0122.1 Nkx3-2 top 2546 seqs: 1.677e-06 (Corrected p-value: 0.0008918)