AME (Analysis of Motif Enrichment): Compiled on Mar  2 2012 at 16:08:25
------------------------------
Copyright (c) Robert McLeay <r.mcleay@imb.uq.edu.au> & Timothy Bailey <t.bailey@imb.uq.edu.au>, 2009.

Command line
ame --oc results/mea_results_ame/Oct4.ame_out --verbose 1 --fix-partition 3760 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_Oct4_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 3760.

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 3760 seqs: 1.591e-229 (Corrected p-value: 8.466e-227)
2. Fisher-exact p-value of motif MA0143.1 Sox2 top 3760 seqs: 5.201e-163 (Corrected p-value: 2.767e-160)
3. Fisher-exact p-value of motif UP00179_1 Pou2f3_3986.2 top 3760 seqs: 2.754e-133 (Corrected p-value: 1.465e-130)
4. Fisher-exact p-value of motif UP00191_1 Pou2f2_3748.1 top 3760 seqs: 6.151e-131 (Corrected p-value: 3.273e-128)
5. Fisher-exact p-value of motif UP00211_1 Pou3f3_3235.2 top 3760 seqs: 1.554e-82 (Corrected p-value: 8.268e-80)
6. Fisher-exact p-value of motif UP00030_1 Sox11_primary top 3760 seqs: 1.395e-52 (Corrected p-value: 7.424e-50)
7. Fisher-exact p-value of motif UP00062_1 Sox4_primary top 3760 seqs: 2.934e-52 (Corrected p-value: 1.561e-49)
8. Fisher-exact p-value of motif MA0039.2 Klf4 top 3760 seqs: 6.464e-50 (Corrected p-value: 3.439e-47)
9. Fisher-exact p-value of motif MA0149.1 EWSR1-FLI1 top 3760 seqs: 1.335e-47 (Corrected p-value: 7.1e-45)
10. Fisher-exact p-value of motif UP00093_1 Klf7_primary top 3760 seqs: 9.152e-43 (Corrected p-value: 4.869e-40)
11. Fisher-exact p-value of motif MA0079.2 SP1 top 3760 seqs: 8.87e-40 (Corrected p-value: 4.719e-37)
12. Fisher-exact p-value of motif UP00002_1 Sp4_primary top 3760 seqs: 2.001e-37 (Corrected p-value: 1.064e-34)
13. Fisher-exact p-value of motif MA0073.1 RREB1 top 3760 seqs: 3.045e-37 (Corrected p-value: 1.62e-34)
14. Fisher-exact p-value of motif UP00021_2 Zfp281_secondary top 3760 seqs: 4.684e-37 (Corrected p-value: 2.492e-34)
15. Fisher-exact p-value of motif UP00099_2 Ascl2_secondary top 3760 seqs: 7.669e-35 (Corrected p-value: 4.08e-32)
16. Fisher-exact p-value of motif UP00033_2 Zfp410_secondary top 3760 seqs: 1.366e-34 (Corrected p-value: 7.268e-32)
17. Fisher-exact p-value of motif UP00021_1 Zfp281_primary top 3760 seqs: 1.175e-30 (Corrected p-value: 6.252e-28)
18. Fisher-exact p-value of motif UP00043_2 Bcl6b_secondary top 3760 seqs: 1.905e-28 (Corrected p-value: 1.014e-25)
19. Fisher-exact p-value of motif UP00015_1 Ehf_primary top 3760 seqs: 4.397e-28 (Corrected p-value: 2.339e-25)
20. Fisher-exact p-value of motif UP00034_1 Sox7_primary top 3760 seqs: 5.129e-28 (Corrected p-value: 2.729e-25)
21. Fisher-exact p-value of motif UP00047_1 Zbtb7b_primary top 3760 seqs: 7.549e-28 (Corrected p-value: 4.016e-25)
22. Fisher-exact p-value of motif UP00408_2 Gabpa_secondary top 3760 seqs: 2.29e-27 (Corrected p-value: 1.219e-24)
23. Fisher-exact p-value of motif UP00097_2 Mtf1_secondary top 3760 seqs: 8.797e-26 (Corrected p-value: 4.68e-23)
24. Fisher-exact p-value of motif UP00061_2 Foxl1_secondary top 3760 seqs: 2.463e-25 (Corrected p-value: 1.31e-22)
25. Fisher-exact p-value of motif UP00061_1 Foxl1_primary top 3760 seqs: 3.348e-24 (Corrected p-value: 1.781e-21)
26. Fisher-exact p-value of motif MA0162.1 Egr1 top 3760 seqs: 1.887e-23 (Corrected p-value: 1.004e-20)
27. Fisher-exact p-value of motif UP00037_1 Zfp105_primary top 3760 seqs: 1.042e-22 (Corrected p-value: 5.542e-20)
28. Fisher-exact p-value of motif UP00088_2 Plagl1_secondary top 3760 seqs: 2.493e-22 (Corrected p-value: 1.326e-19)
29. Fisher-exact p-value of motif UP00000_2 Smad3_secondary top 3760 seqs: 5.53e-22 (Corrected p-value: 2.942e-19)
30. Fisher-exact p-value of motif UP00022_2 Zfp740_secondary top 3760 seqs: 1.212e-21 (Corrected p-value: 6.45e-19)
31. Fisher-exact p-value of motif UP00101_2 Sox12_secondary top 3760 seqs: 2.914e-21 (Corrected p-value: 1.55e-18)
32. Fisher-exact p-value of motif MA0004.1 Arnt top 3760 seqs: 1.652e-20 (Corrected p-value: 8.787e-18)
33. Fisher-exact p-value of motif MA0104.1 Mycn top 3760 seqs: 1.652e-20 (Corrected p-value: 8.787e-18)
34. Fisher-exact p-value of motif MA0093.1 USF1 top 3760 seqs: 1.652e-20 (Corrected p-value: 8.787e-18)
35. Fisher-exact p-value of motif UP00096_2 Sox13_secondary top 3760 seqs: 1.66e-20 (Corrected p-value: 8.833e-18)
36. Fisher-exact p-value of motif UP00024_1 Glis2_primary top 3760 seqs: 1.666e-20 (Corrected p-value: 8.865e-18)
37. Fisher-exact p-value of motif UP00407_1 Elf3_primary top 3760 seqs: 3.148e-20 (Corrected p-value: 1.675e-17)
38. Fisher-exact p-value of motif UP00101_1 Sox12_primary top 3760 seqs: 3.255e-20 (Corrected p-value: 1.731e-17)
39. Fisher-exact p-value of motif MA0062.1 GABPA top 3760 seqs: 3.708e-20 (Corrected p-value: 1.973e-17)
40. Fisher-exact p-value of motif UP00029_1 Tbp_primary top 3760 seqs: 1.287e-19 (Corrected p-value: 6.848e-17)
41. Fisher-exact p-value of motif MA0148.1 FOXA1 top 3760 seqs: 1.572e-19 (Corrected p-value: 8.362e-17)
42. Fisher-exact p-value of motif MA0084.1 SRY top 3760 seqs: 4.394e-19 (Corrected p-value: 2.338e-16)
43. Fisher-exact p-value of motif MA0039.1 Klf4 top 3760 seqs: 5.397e-19 (Corrected p-value: 2.871e-16)
44. Fisher-exact p-value of motif UP00073_1 Foxa2_primary top 3760 seqs: 6.529e-19 (Corrected p-value: 3.474e-16)
45. Fisher-exact p-value of motif MA0062.2 GABPA top 3760 seqs: 7.179e-19 (Corrected p-value: 3.819e-16)
46. Fisher-exact p-value of motif UP00025_1 Foxk1_primary top 3760 seqs: 8.861e-18 (Corrected p-value: 4.714e-15)
47. Fisher-exact p-value of motif MA0047.2 Foxa2 top 3760 seqs: 1.213e-17 (Corrected p-value: 6.454e-15)
48. Fisher-exact p-value of motif UP00085_1 Sfpi1_primary top 3760 seqs: 3.059e-17 (Corrected p-value: 1.627e-14)
49. Fisher-exact p-value of motif MA0079.1 SP1 top 3760 seqs: 4.397e-17 (Corrected p-value: 2.339e-14)
50. Fisher-exact p-value of motif MA0041.1 Foxd3 top 3760 seqs: 4.977e-17 (Corrected p-value: 2.648e-14)
51. Fisher-exact p-value of motif UP00039_1 Foxj3_primary top 3760 seqs: 5.793e-17 (Corrected p-value: 3.082e-14)
52. Fisher-exact p-value of motif MA0137.1 STAT1 top 3760 seqs: 8.02e-17 (Corrected p-value: 4.266e-14)
53. Fisher-exact p-value of motif UP00077_2 Srf_secondary top 3760 seqs: 1.768e-16 (Corrected p-value: 9.406e-14)
54. Fisher-exact p-value of motif MA0136.1 ELF5 top 3760 seqs: 4.601e-16 (Corrected p-value: 2.448e-13)
55. Fisher-exact p-value of motif MA0144.1 Stat3 top 3760 seqs: 4.857e-16 (Corrected p-value: 2.584e-13)
56. Fisher-exact p-value of motif MA0068.1 Pax4 top 3760 seqs: 7.759e-16 (Corrected p-value: 4.128e-13)
57. Fisher-exact p-value of motif UP00035_2 Hic1_secondary top 3760 seqs: 1.522e-15 (Corrected p-value: 8.099e-13)
58. Fisher-exact p-value of motif MA0156.1 FEV top 3760 seqs: 3.58e-15 (Corrected p-value: 1.905e-12)
59. Fisher-exact p-value of motif MA0087.1 Sox5 top 3760 seqs: 6.494e-15 (Corrected p-value: 3.455e-12)
60. Fisher-exact p-value of motif UP00042_2 Gm397_secondary top 3760 seqs: 2.268e-14 (Corrected p-value: 1.207e-11)
61. Fisher-exact p-value of motif UP00086_1 Irf3_primary top 3760 seqs: 2.775e-14 (Corrected p-value: 1.477e-11)
62. Fisher-exact p-value of motif MA0042.1 FOXI1 top 3760 seqs: 5.157e-14 (Corrected p-value: 2.743e-11)
63. Fisher-exact p-value of motif UP00073_2 Foxa2_secondary top 3760 seqs: 6.588e-14 (Corrected p-value: 3.505e-11)
64. Fisher-exact p-value of motif UP00023_1 Sox30_primary top 3760 seqs: 1.005e-13 (Corrected p-value: 5.346e-11)
65. Fisher-exact p-value of motif MA0137.2 STAT1 top 3760 seqs: 2.088e-13 (Corrected p-value: 1.111e-10)
66. Fisher-exact p-value of motif MA0019.1 Ddit3::Cebpa top 3760 seqs: 4.788e-13 (Corrected p-value: 2.547e-10)
67. Fisher-exact p-value of motif MA0080.2 SPI1 top 3760 seqs: 7.59e-13 (Corrected p-value: 4.038e-10)
68. Fisher-exact p-value of motif MA0164.1 Nr2e3 top 3760 seqs: 1.133e-12 (Corrected p-value: 6.027e-10)
69. Fisher-exact p-value of motif UP00075_1 Sox15_primary top 3760 seqs: 1.187e-12 (Corrected p-value: 6.313e-10)
70. Fisher-exact p-value of motif UP00007_1 Egr1_primary top 3760 seqs: 2.602e-12 (Corrected p-value: 1.384e-09)
71. Fisher-exact p-value of motif MA0033.1 FOXL1 top 3760 seqs: 3.108e-12 (Corrected p-value: 1.654e-09)
72. Fisher-exact p-value of motif UP00051_1 Sox8_primary top 3760 seqs: 4.1e-12 (Corrected p-value: 2.181e-09)
73. Fisher-exact p-value of motif UP00064_1 Sox18_primary top 3760 seqs: 7.304e-12 (Corrected p-value: 3.886e-09)
74. Fisher-exact p-value of motif MA0105.1 NFKB1 top 3760 seqs: 8.463e-12 (Corrected p-value: 4.502e-09)
75. Fisher-exact p-value of motif UP00006_2 Zic3_secondary top 3760 seqs: 8.709e-12 (Corrected p-value: 4.633e-09)
76. Fisher-exact p-value of motif MA0104.2 Mycn top 3760 seqs: 3.071e-11 (Corrected p-value: 1.634e-08)
77. Fisher-exact p-value of motif UP00041_1 Foxj1_primary top 3760 seqs: 3.957e-11 (Corrected p-value: 2.105e-08)
78. Fisher-exact p-value of motif UP00060_1 Max_primary top 3760 seqs: 5.121e-11 (Corrected p-value: 2.724e-08)
79. Fisher-exact p-value of motif UP00408_1 Gabpa_primary top 3760 seqs: 9.574e-11 (Corrected p-value: 5.093e-08)
80. Fisher-exact p-value of motif UP00255_1 Dbx1_3486.1 top 3760 seqs: 1.699e-10 (Corrected p-value: 9.038e-08)
81. Fisher-exact p-value of motif UP00071_1 Sox21_primary top 3760 seqs: 1.845e-10 (Corrected p-value: 9.814e-08)
82. Fisher-exact p-value of motif MA0055.1 Myf top 3760 seqs: 1.885e-10 (Corrected p-value: 1.003e-07)
83. Fisher-exact p-value of motif UP00129_1 Pou3f1_3819.1 top 3760 seqs: 2.057e-10 (Corrected p-value: 1.094e-07)
84. Fisher-exact p-value of motif MA0030.1 FOXF2 top 3760 seqs: 2.902e-10 (Corrected p-value: 1.544e-07)
85. Fisher-exact p-value of motif UP00094_2 Zfp128_secondary top 3760 seqs: 4.91e-10 (Corrected p-value: 2.612e-07)
86. Fisher-exact p-value of motif MA0152.1 NFATC2 top 3760 seqs: 1.017e-09 (Corrected p-value: 5.409e-07)
87. Fisher-exact p-value of motif UP00102_2 Zic1_secondary top 3760 seqs: 1.136e-09 (Corrected p-value: 6.042e-07)
88. Fisher-exact p-value of motif MA0116.1 Zfp423 top 3760 seqs: 1.333e-09 (Corrected p-value: 7.09e-07)
89. Fisher-exact p-value of motif UP00016_1 Sry_primary top 3760 seqs: 1.681e-09 (Corrected p-value: 8.943e-07)
90. Fisher-exact p-value of motif UP00254_1 Pou2f1_3081.2 top 3760 seqs: 1.905e-09 (Corrected p-value: 1.013e-06)
91. Fisher-exact p-value of motif MA0052.1 MEF2A top 3760 seqs: 4.244e-09 (Corrected p-value: 2.258e-06)
92. Fisher-exact p-value of motif UP00244_1 Tlx2_3498.2 top 3760 seqs: 4.295e-09 (Corrected p-value: 2.285e-06)
93. Fisher-exact p-value of motif MA0058.1 MAX top 3760 seqs: 4.352e-09 (Corrected p-value: 2.315e-06)
94. Fisher-exact p-value of motif UP00022_1 Zfp740_primary top 3760 seqs: 4.53e-09 (Corrected p-value: 2.41e-06)
95. Fisher-exact p-value of motif UP00165_1 Titf1_1722.2 top 3760 seqs: 4.601e-09 (Corrected p-value: 2.448e-06)
96. Fisher-exact p-value of motif UP00039_2 Foxj3_secondary top 3760 seqs: 6.728e-09 (Corrected p-value: 3.579e-06)
97. Fisher-exact p-value of motif UP00057_2 Zic2_secondary top 3760 seqs: 7.506e-09 (Corrected p-value: 3.993e-06)
98. Fisher-exact p-value of motif UP00158_1 Pou1f1_3818.1 top 3760 seqs: 8.454e-09 (Corrected p-value: 4.497e-06)
99. Fisher-exact p-value of motif MA0077.1 SOX9 top 3760 seqs: 9.395e-09 (Corrected p-value: 4.998e-06)
100. Fisher-exact p-value of motif UP00091_1 Sox5_primary top 3760 seqs: 9.969e-09 (Corrected p-value: 5.304e-06)
101. Fisher-exact p-value of motif UP00036_2 Myf6_secondary top 3760 seqs: 1.501e-08 (Corrected p-value: 7.984e-06)
102. Fisher-exact p-value of motif UP00105_1 Pou3f4_3773.1 top 3760 seqs: 2.1e-08 (Corrected p-value: 1.117e-05)
103. Fisher-exact p-value of motif MA0050.1 IRF1 top 3760 seqs: 2.231e-08 (Corrected p-value: 1.187e-05)
104. Fisher-exact p-value of motif UP00065_1 Zfp161_primary top 3760 seqs: 2.751e-08 (Corrected p-value: 1.464e-05)
105. Fisher-exact p-value of motif MA0259.1 HIF1A::ARNT top 3760 seqs: 2.869e-08 (Corrected p-value: 1.526e-05)
106. Fisher-exact p-value of motif MA0157.1 FOXO3 top 3760 seqs: 3.457e-08 (Corrected p-value: 1.839e-05)
107. Fisher-exact p-value of motif UP00149_1 Phox2b_3948.1 top 3760 seqs: 3.88e-08 (Corrected p-value: 2.064e-05)
108. Fisher-exact p-value of motif UP00028_2 Tcfap2e_secondary top 3760 seqs: 4.263e-08 (Corrected p-value: 2.268e-05)
109. Fisher-exact p-value of motif MA0090.1 TEAD1 top 3760 seqs: 4.405e-08 (Corrected p-value: 2.343e-05)
110. Fisher-exact p-value of motif MA0088.1 znf143 top 3760 seqs: 5.77e-08 (Corrected p-value: 3.07e-05)
111. Fisher-exact p-value of motif UP00088_1 Plagl1_primary top 3760 seqs: 7.356e-08 (Corrected p-value: 3.913e-05)
112. Fisher-exact p-value of motif UP00002_2 Sp4_secondary top 3760 seqs: 7.885e-08 (Corrected p-value: 4.195e-05)
113. Fisher-exact p-value of motif MA0081.1 SPIB top 3760 seqs: 9.636e-08 (Corrected p-value: 5.126e-05)
114. Fisher-exact p-value of motif UP00004_2 Sox14_secondary top 3760 seqs: 1.206e-07 (Corrected p-value: 6.418e-05)
115. Fisher-exact p-value of motif MA0160.1 NR4A2 top 3760 seqs: 1.33e-07 (Corrected p-value: 7.076e-05)
116. Fisher-exact p-value of motif MA0047.1 Foxa2 top 3760 seqs: 1.343e-07 (Corrected p-value: 7.147e-05)
117. Fisher-exact p-value of motif UP00406_1 Spdef_primary top 3760 seqs: 1.657e-07 (Corrected p-value: 8.815e-05)
118. Fisher-exact p-value of motif MA0078.1 Sox17 top 3760 seqs: 1.751e-07 (Corrected p-value: 9.317e-05)
119. Fisher-exact p-value of motif UP00118_1 Pou4f3_2791.1 top 3760 seqs: 2.079e-07 (Corrected p-value: 0.0001106)
120. Fisher-exact p-value of motif UP00047_2 Zbtb7b_secondary top 3760 seqs: 2.799e-07 (Corrected p-value: 0.0001489)
121. Fisher-exact p-value of motif MA0102.1 Cebpa top 3760 seqs: 3.19e-07 (Corrected p-value: 0.0001697)
122. Fisher-exact p-value of motif UP00249_1 Nkx2-5_3436.1 top 3760 seqs: 4.004e-07 (Corrected p-value: 0.000213)
123. Fisher-exact p-value of motif UP00029_2 Tbp_secondary top 3760 seqs: 6.384e-07 (Corrected p-value: 0.0003396)
124. Fisher-exact p-value of motif UP00172_1 Prop1_3949.1 top 3760 seqs: 7.064e-07 (Corrected p-value: 0.0003758)
125. Fisher-exact p-value of motif UP00046_1 Tcfe2a_primary top 3760 seqs: 1.042e-06 (Corrected p-value: 0.000554)
126. Fisher-exact p-value of motif MA0002.2 RUNX1 top 3760 seqs: 1.235e-06 (Corrected p-value: 0.000657)
127. Fisher-exact p-value of motif MA0108.1 TBP top 3760 seqs: 1.308e-06 (Corrected p-value: 0.0006958)
128. Fisher-exact p-value of motif UP00050_1 Bhlhb2_primary top 3760 seqs: 1.312e-06 (Corrected p-value: 0.0006977)
129. Fisher-exact p-value of motif MA0102.2 CEBPA top 3760 seqs: 1.447e-06 (Corrected p-value: 0.0007696)
130. Fisher-exact p-value of motif MA0070.1 PBX1 top 3760 seqs: 1.613e-06 (Corrected p-value: 0.000858)