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

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.

Command line
ame --oc results/mea_results_ame/Sox2.ame_out --verbose 1 --fix-partition 4526 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_Sox2_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 4526.

Threshold p-value for reporting results: 0.001
Motif p-values are corrected by #Motifs × #ThresholdsTested – (532 × 1 = 532)

motif numberscoring methodmotif namesecondary motif namescored sequencesp-valuecorrected p-value
1.Fisher-exact testUP00062_1Sox4_primarytop 4526 seqs1.86e-2319.898e-229
2.Fisher-exact testUP00030_1Sox11_primarytop 4526 seqs3.248e-2301.728e-227
3.Fisher-exact testMA0143.1Sox2top 4526 seqs1.226e-2186.524e-216
4.Fisher-exact testMA0142.1Pou5f1top 4526 seqs4.169e-1822.218e-179
5.Fisher-exact testMA0077.1SOX9top 4526 seqs1.455e-1357.743e-133
6.Fisher-exact testUP00034_1Sox7_primarytop 4526 seqs1.585e-1268.432e-124
7.Fisher-exact testUP00023_1Sox30_primarytop 4526 seqs1.126e-1055.99e-103
8.Fisher-exact testUP00016_2Sry_secondarytop 4526 seqs1.03e-1015.482e-99
9.Fisher-exact testUP00179_1Pou2f3_3986.2top 4526 seqs2.727e-961.451e-93
10.Fisher-exact testUP00101_1Sox12_primarytop 4526 seqs1.587e-958.445e-93
11.Fisher-exact testUP00191_1Pou2f2_3748.1top 4526 seqs1.081e-885.751e-86
12.Fisher-exact testUP00004_2Sox14_secondarytop 4526 seqs2.371e-861.261e-83
13.Fisher-exact testUP00075_1Sox15_primarytop 4526 seqs8.879e-804.724e-77
14.Fisher-exact testUP00093_1Klf7_primarytop 4526 seqs2.185e-771.163e-74
15.Fisher-exact testMA0039.2Klf4top 4526 seqs3.707e-751.972e-72
16.Fisher-exact testUP00101_2Sox12_secondarytop 4526 seqs5.718e-643.042e-61
17.Fisher-exact testUP00064_1Sox18_primarytop 4526 seqs1.732e-639.215e-61
18.Fisher-exact testMA0149.1EWSR1-FLI1top 4526 seqs3.011e-561.602e-53
19.Fisher-exact testUP00099_2Ascl2_secondarytop 4526 seqs7.012e-553.731e-52
20.Fisher-exact testMA0078.1Sox17top 4526 seqs2.61e-531.388e-50
21.Fisher-exact testUP00091_1Sox5_primarytop 4526 seqs3.493e-511.859e-48
22.Fisher-exact testUP00051_1Sox8_primarytop 4526 seqs2.345e-501.247e-47
23.Fisher-exact testUP00002_1Sp4_primarytop 4526 seqs7.462e-503.97e-47
24.Fisher-exact testUP00071_2Sox21_secondarytop 4526 seqs2.166e-491.153e-46
25.Fisher-exact testUP00033_2Zfp410_secondarytop 4526 seqs1.887e-471.004e-44
26.Fisher-exact testMA0079.2SP1top 4526 seqs5.255e-472.796e-44
27.Fisher-exact testMA0084.1SRYtop 4526 seqs2.588e-451.377e-42
28.Fisher-exact testUP00021_2Zfp281_secondarytop 4526 seqs1.62e-408.619e-38
29.Fisher-exact testUP00061_2Foxl1_secondarytop 4526 seqs7.893e-404.199e-37
30.Fisher-exact testUP00021_1Zfp281_primarytop 4526 seqs1.246e-386.631e-36
31.Fisher-exact testUP00073_2Foxa2_secondarytop 4526 seqs7.684e-344.088e-31
32.Fisher-exact testUP00043_2Bcl6b_secondarytop 4526 seqs6.291e-333.347e-30
33.Fisher-exact testUP00061_1Foxl1_primarytop 4526 seqs1.017e-325.412e-30
34.Fisher-exact testUP00055_2Hbp1_secondarytop 4526 seqs6.245e-313.322e-28
35.Fisher-exact testMA0162.1Egr1top 4526 seqs1.589e-308.453e-28
36.Fisher-exact testUP00211_1Pou3f3_3235.2top 4526 seqs2.015e-301.072e-27
37.Fisher-exact testMA0087.1Sox5top 4526 seqs2.196e-301.169e-27
38.Fisher-exact testUP00102_2Zic1_secondarytop 4526 seqs2.267e-301.206e-27
39.Fisher-exact testUP00057_2Zic2_secondarytop 4526 seqs5.948e-303.164e-27
40.Fisher-exact testUP00096_1Sox13_primarytop 4526 seqs1.663e-298.845e-27
41.Fisher-exact testUP00073_1Foxa2_primarytop 4526 seqs4.432e-292.358e-26
42.Fisher-exact testUP00041_1Foxj1_primarytop 4526 seqs1.231e-276.546e-25
43.Fisher-exact testUP00000_2Smad3_secondarytop 4526 seqs1.551e-278.251e-25
44.Fisher-exact testMA0042.1FOXI1top 4526 seqs1.836e-279.769e-25
45.Fisher-exact testMA0073.1RREB1top 4526 seqs9.356e-274.977e-24
46.Fisher-exact testUP00025_1Foxk1_primarytop 4526 seqs4.021e-262.139e-23
47.Fisher-exact testUP00047_1Zbtb7b_primarytop 4526 seqs9.695e-265.158e-23
48.Fisher-exact testUP00039_1Foxj3_primarytop 4526 seqs1.608e-258.556e-23
49.Fisher-exact testUP00408_2Gabpa_secondarytop 4526 seqs3.634e-251.933e-22
50.Fisher-exact testUP00006_2Zic3_secondarytop 4526 seqs2.683e-241.427e-21
51.Fisher-exact testUP00029_1Tbp_primarytop 4526 seqs2.552e-231.358e-20
52.Fisher-exact testMA0041.1Foxd3top 4526 seqs1.539e-228.187e-20
53.Fisher-exact testUP00037_1Zfp105_primarytop 4526 seqs4.042e-212.151e-18
54.Fisher-exact testMA0079.1SP1top 4526 seqs1.762e-209.373e-18
55.Fisher-exact testMA0030.1FOXF2top 4526 seqs2.416e-201.285e-17
56.Fisher-exact testUP00014_1Sox17_primarytop 4526 seqs4.695e-202.498e-17
57.Fisher-exact testMA0136.1ELF5top 4526 seqs1.298e-196.904e-17
58.Fisher-exact testMA0062.1GABPAtop 4526 seqs3.345e-191.78e-16
59.Fisher-exact testMA0039.1Klf4top 4526 seqs1.536e-188.169e-16
60.Fisher-exact testMA0019.1Ddit3::Cebpatop 4526 seqs2.132e-181.134e-15
61.Fisher-exact testMA0157.1FOXO3top 4526 seqs2.38e-181.266e-15
62.Fisher-exact testUP00042_2Gm397_secondarytop 4526 seqs3.013e-181.603e-15
63.Fisher-exact testMA0148.1FOXA1top 4526 seqs5.216e-182.775e-15
64.Fisher-exact testUP00007_1Egr1_primarytop 4526 seqs6.565e-183.493e-15
65.Fisher-exact testUP00039_2Foxj3_secondarytop 4526 seqs8.285e-184.408e-15
66.Fisher-exact testUP00097_2Mtf1_secondarytop 4526 seqs8.468e-184.505e-15
67.Fisher-exact testUP00077_2Srf_secondarytop 4526 seqs7.623e-174.055e-14
68.Fisher-exact testMA0080.2SPI1top 4526 seqs3.278e-161.744e-13
69.Fisher-exact testMA0156.1FEVtop 4526 seqs3.674e-161.954e-13
70.Fisher-exact testUP00015_1Ehf_primarytop 4526 seqs4.117e-162.19e-13
71.Fisher-exact testUP00071_1Sox21_primarytop 4526 seqs1.862e-159.905e-13
72.Fisher-exact testUP00099_1Ascl2_primarytop 4526 seqs4.822e-152.565e-12
73.Fisher-exact testMA0062.2GABPAtop 4526 seqs1.108e-145.895e-12
74.Fisher-exact testUP00069_2Sox1_secondarytop 4526 seqs1.864e-149.918e-12
75.Fisher-exact testMA0164.1Nr2e3top 4526 seqs2.056e-141.094e-11
76.Fisher-exact testMA0047.2Foxa2top 4526 seqs2.224e-141.183e-11
77.Fisher-exact testUP00407_1Elf3_primarytop 4526 seqs2.983e-141.587e-11
78.Fisher-exact testMA0102.1Cebpatop 4526 seqs5.134e-142.731e-11
79.Fisher-exact testUP00066_2Hnf4a_secondarytop 4526 seqs8.328e-144.431e-11
80.Fisher-exact testMA0144.1Stat3top 4526 seqs9.674e-145.147e-11
81.Fisher-exact testUP00088_2Plagl1_secondarytop 4526 seqs1.822e-139.694e-11
82.Fisher-exact testUP00022_2Zfp740_secondarytop 4526 seqs2.665e-131.418e-10
83.Fisher-exact testMA0004.1Arnttop 4526 seqs2.756e-131.466e-10
84.Fisher-exact testMA0093.1USF1top 4526 seqs2.756e-131.466e-10
85.Fisher-exact testMA0104.1Mycntop 4526 seqs2.756e-131.466e-10
86.Fisher-exact testUP00016_1Sry_primarytop 4526 seqs3.888e-132.069e-10
87.Fisher-exact testUP00214_1Hoxb5_3122.2top 4526 seqs4.962e-132.64e-10
88.Fisher-exact testMA0068.1Pax4top 4526 seqs7.189e-133.824e-10
89.Fisher-exact testMA0105.1NFKB1top 4526 seqs8.979e-134.777e-10
90.Fisher-exact testMA0137.2STAT1top 4526 seqs1.849e-129.838e-10
91.Fisher-exact testUP00096_2Sox13_secondarytop 4526 seqs4.481e-122.384e-09
92.Fisher-exact testUP00182_1Hoxa6_1040.1top 4526 seqs4.523e-122.406e-09
93.Fisher-exact testUP00035_2Hic1_secondarytop 4526 seqs6.037e-123.211e-09
94.Fisher-exact testUP00391_1Hoxa3_primarytop 4526 seqs6.772e-123.603e-09
95.Fisher-exact testUP00022_1Zfp740_primarytop 4526 seqs1.152e-116.131e-09
96.Fisher-exact testMA0033.1FOXL1top 4526 seqs1.511e-118.041e-09
97.Fisher-exact testUP00255_1Dbx1_3486.1top 4526 seqs1.516e-118.067e-09
98.Fisher-exact testUP00044_2Mafk_secondarytop 4526 seqs2.215e-111.178e-08
99.Fisher-exact testMA0040.1Foxq1top 4526 seqs2.755e-111.465e-08
100.Fisher-exact testUP00002_2Sp4_secondarytop 4526 seqs3.243e-111.725e-08
101.Fisher-exact testUP00083_1Tcf7l2_primarytop 4526 seqs4.186e-112.227e-08
102.Fisher-exact testUP00088_1Plagl1_primarytop 4526 seqs5.102e-112.714e-08
103.Fisher-exact testMA0070.1PBX1top 4526 seqs8.079e-114.298e-08
104.Fisher-exact testUP00024_1Glis2_primarytop 4526 seqs8.386e-114.461e-08
105.Fisher-exact testUP00054_1Tcf7_primarytop 4526 seqs1.204e-106.403e-08
106.Fisher-exact testMA0055.1Myftop 4526 seqs1.523e-108.103e-08
107.Fisher-exact testMA0048.1NHLH1top 4526 seqs1.802e-109.584e-08
108.Fisher-exact testUP00189_1Hoxa5_3415.1top 4526 seqs2.794e-101.486e-07
109.Fisher-exact testUP00105_1Pou3f4_3773.1top 4526 seqs3.719e-101.979e-07
110.Fisher-exact testMA0090.1TEAD1top 4526 seqs4.172e-102.219e-07
111.Fisher-exact testUP00094_2Zfp128_secondarytop 4526 seqs5.149e-102.74e-07
112.Fisher-exact testMA0116.1Zfp423top 4526 seqs5.634e-102.997e-07
113.Fisher-exact testMA0002.2RUNX1top 4526 seqs5.963e-103.172e-07
114.Fisher-exact testUP00254_1Pou2f1_3081.2top 4526 seqs7.163e-103.811e-07
115.Fisher-exact testUP00227_1Duxl_1286.2top 4526 seqs9.272e-104.933e-07
116.Fisher-exact testUP00004_1Sox14_primarytop 4526 seqs1.277e-096.792e-07
117.Fisher-exact testMA0065.2PPARG::RXRAtop 4526 seqs1.308e-096.959e-07
118.Fisher-exact testMA0102.2CEBPAtop 4526 seqs1.778e-099.458e-07
119.Fisher-exact testUP00164_1Hoxa7_2668.2top 4526 seqs2.56e-091.362e-06
120.Fisher-exact testUP00036_2Myf6_secondarytop 4526 seqs2.676e-091.424e-06
121.Fisher-exact testMA0058.1MAXtop 4526 seqs3.407e-091.813e-06
122.Fisher-exact testUP00408_1Gabpa_primarytop 4526 seqs4.43e-092.357e-06
123.Fisher-exact testUP00046_1Tcfe2a_primarytop 4526 seqs4.839e-092.575e-06
124.Fisher-exact testUP00174_1Hoxa2_3079.1top 4526 seqs4.901e-092.607e-06
125.Fisher-exact testUP00242_1Hoxc8_3429.2top 4526 seqs5.285e-092.812e-06
126.Fisher-exact testMA0052.1MEF2Atop 4526 seqs6.875e-093.657e-06
127.Fisher-exact testUP00231_1Nkx2-2_2823.1top 4526 seqs7.19e-093.825e-06
128.Fisher-exact testUP00165_1Titf1_1722.2top 4526 seqs8.321e-094.427e-06
129.Fisher-exact testUP00058_1Tcf3_primarytop 4526 seqs1.022e-085.436e-06
130.Fisher-exact testUP00085_1Sfpi1_primarytop 4526 seqs1.029e-085.473e-06
131.Fisher-exact testUP00067_1Lef1_primarytop 4526 seqs2.937e-081.562e-05
132.Fisher-exact testMA0137.1STAT1top 4526 seqs3.721e-081.98e-05
133.Fisher-exact testUP00121_1Hoxd10_2368.2top 4526 seqs3.909e-082.08e-05
134.Fisher-exact testMA0069.1Pax6top 4526 seqs4.076e-082.169e-05
135.Fisher-exact testUP00158_1Pou1f1_3818.1top 4526 seqs4.972e-082.645e-05
136.Fisher-exact testUP00124_1Ipf1_3815.1top 4526 seqs6.434e-083.423e-05
137.Fisher-exact testMA0259.1HIF1A::ARNTtop 4526 seqs7.116e-083.786e-05
138.Fisher-exact testUP00252_1Hoxc5_2630.2top 4526 seqs8.96e-084.767e-05
139.Fisher-exact testUP00260_1Hoxc6_3954.2top 4526 seqs9.611e-085.113e-05
140.Fisher-exact testUP00023_2Sox30_secondarytop 4526 seqs1.696e-079.021e-05
141.Fisher-exact testUP00079_1Esrra_primarytop 4526 seqs1.819e-079.677e-05
142.Fisher-exact testUP00110_1Dlx4_3488.2top 4526 seqs1.854e-079.86e-05
143.Fisher-exact testMA0060.1NFYAtop 4526 seqs2.005e-070.0001067
144.Fisher-exact testUP00200_2Nkx6-1_2825.2top 4526 seqs2.51e-070.0001335
145.Fisher-exact testUP00249_1Nkx2-5_3436.1top 4526 seqs2.773e-070.0001475
146.Fisher-exact testUP00188_1Lmx1a_2238.2top 4526 seqs3.224e-070.0001715
147.Fisher-exact testUP00169_1Lmx1b_3433.2top 4526 seqs3.841e-070.0002043
148.Fisher-exact testUP00154_1Dlx3_1030.1top 4526 seqs4.353e-070.0002316
149.Fisher-exact testMA0088.1znf143top 4526 seqs4.453e-070.0002369
150.Fisher-exact testUP00107_1Nkx2-4_3074.1top 4526 seqs4.488e-070.0002387
151.Fisher-exact testUP00127_1Gsh2_3990.2top 4526 seqs5.851e-070.0003112
152.Fisher-exact testMA0104.2Mycntop 4526 seqs6.495e-070.0003455
153.Fisher-exact testUP00244_1Tlx2_3498.2top 4526 seqs6.798e-070.0003616
154.Fisher-exact testUP00037_2Zfp105_secondarytop 4526 seqs7.086e-070.0003769
155.Fisher-exact testUP00129_1Pou3f1_3819.1top 4526 seqs7.094e-070.0003773
156.Fisher-exact testMA0047.1Foxa2top 4526 seqs7.249e-070.0003856
157.Fisher-exact testUP00024_2Glis2_secondarytop 4526 seqs7.935e-070.0004221
158.Fisher-exact testMA0081.1SPIBtop 4526 seqs1.006e-060.0005349
159.Fisher-exact testUP00391_3Hoxa3_2783.2top 4526 seqs1.014e-060.0005393
160.Fisher-exact testMA0135.1Lhx3top 4526 seqs1.019e-060.0005418
161.Fisher-exact testUP00217_1Hoxa10_2318.1top 4526 seqs1.082e-060.0005755