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/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)

motif numberscoring methodmotif namesecondary motif namescored sequencesp-valuecorrected p-value
1.Fisher-exact testMA0142.1Pou5f1top 3760 seqs1.591e-2298.466e-227
2.Fisher-exact testMA0143.1Sox2top 3760 seqs5.201e-1632.767e-160
3.Fisher-exact testUP00179_1Pou2f3_3986.2top 3760 seqs2.754e-1331.465e-130
4.Fisher-exact testUP00191_1Pou2f2_3748.1top 3760 seqs6.151e-1313.273e-128
5.Fisher-exact testUP00211_1Pou3f3_3235.2top 3760 seqs1.554e-828.268e-80
6.Fisher-exact testUP00030_1Sox11_primarytop 3760 seqs1.395e-527.424e-50
7.Fisher-exact testUP00062_1Sox4_primarytop 3760 seqs2.934e-521.561e-49
8.Fisher-exact testMA0039.2Klf4top 3760 seqs6.464e-503.439e-47
9.Fisher-exact testMA0149.1EWSR1-FLI1top 3760 seqs1.335e-477.1e-45
10.Fisher-exact testUP00093_1Klf7_primarytop 3760 seqs9.152e-434.869e-40
11.Fisher-exact testMA0079.2SP1top 3760 seqs8.87e-404.719e-37
12.Fisher-exact testUP00002_1Sp4_primarytop 3760 seqs2.001e-371.064e-34
13.Fisher-exact testMA0073.1RREB1top 3760 seqs3.045e-371.62e-34
14.Fisher-exact testUP00021_2Zfp281_secondarytop 3760 seqs4.684e-372.492e-34
15.Fisher-exact testUP00099_2Ascl2_secondarytop 3760 seqs7.669e-354.08e-32
16.Fisher-exact testUP00033_2Zfp410_secondarytop 3760 seqs1.366e-347.268e-32
17.Fisher-exact testUP00021_1Zfp281_primarytop 3760 seqs1.175e-306.252e-28
18.Fisher-exact testUP00043_2Bcl6b_secondarytop 3760 seqs1.905e-281.014e-25
19.Fisher-exact testUP00015_1Ehf_primarytop 3760 seqs4.397e-282.339e-25
20.Fisher-exact testUP00034_1Sox7_primarytop 3760 seqs5.129e-282.729e-25
21.Fisher-exact testUP00047_1Zbtb7b_primarytop 3760 seqs7.549e-284.016e-25
22.Fisher-exact testUP00408_2Gabpa_secondarytop 3760 seqs2.29e-271.219e-24
23.Fisher-exact testUP00097_2Mtf1_secondarytop 3760 seqs8.797e-264.68e-23
24.Fisher-exact testUP00061_2Foxl1_secondarytop 3760 seqs2.463e-251.31e-22
25.Fisher-exact testUP00061_1Foxl1_primarytop 3760 seqs3.348e-241.781e-21
26.Fisher-exact testMA0162.1Egr1top 3760 seqs1.887e-231.004e-20
27.Fisher-exact testUP00037_1Zfp105_primarytop 3760 seqs1.042e-225.542e-20
28.Fisher-exact testUP00088_2Plagl1_secondarytop 3760 seqs2.493e-221.326e-19
29.Fisher-exact testUP00000_2Smad3_secondarytop 3760 seqs5.53e-222.942e-19
30.Fisher-exact testUP00022_2Zfp740_secondarytop 3760 seqs1.212e-216.45e-19
31.Fisher-exact testUP00101_2Sox12_secondarytop 3760 seqs2.914e-211.55e-18
32.Fisher-exact testMA0004.1Arnttop 3760 seqs1.652e-208.787e-18
33.Fisher-exact testMA0104.1Mycntop 3760 seqs1.652e-208.787e-18
34.Fisher-exact testMA0093.1USF1top 3760 seqs1.652e-208.787e-18
35.Fisher-exact testUP00096_2Sox13_secondarytop 3760 seqs1.66e-208.833e-18
36.Fisher-exact testUP00024_1Glis2_primarytop 3760 seqs1.666e-208.865e-18
37.Fisher-exact testUP00407_1Elf3_primarytop 3760 seqs3.148e-201.675e-17
38.Fisher-exact testUP00101_1Sox12_primarytop 3760 seqs3.255e-201.731e-17
39.Fisher-exact testMA0062.1GABPAtop 3760 seqs3.708e-201.973e-17
40.Fisher-exact testUP00029_1Tbp_primarytop 3760 seqs1.287e-196.848e-17
41.Fisher-exact testMA0148.1FOXA1top 3760 seqs1.572e-198.362e-17
42.Fisher-exact testMA0084.1SRYtop 3760 seqs4.394e-192.338e-16
43.Fisher-exact testMA0039.1Klf4top 3760 seqs5.397e-192.871e-16
44.Fisher-exact testUP00073_1Foxa2_primarytop 3760 seqs6.529e-193.474e-16
45.Fisher-exact testMA0062.2GABPAtop 3760 seqs7.179e-193.819e-16
46.Fisher-exact testUP00025_1Foxk1_primarytop 3760 seqs8.861e-184.714e-15
47.Fisher-exact testMA0047.2Foxa2top 3760 seqs1.213e-176.454e-15
48.Fisher-exact testUP00085_1Sfpi1_primarytop 3760 seqs3.059e-171.627e-14
49.Fisher-exact testMA0079.1SP1top 3760 seqs4.397e-172.339e-14
50.Fisher-exact testMA0041.1Foxd3top 3760 seqs4.977e-172.648e-14
51.Fisher-exact testUP00039_1Foxj3_primarytop 3760 seqs5.793e-173.082e-14
52.Fisher-exact testMA0137.1STAT1top 3760 seqs8.02e-174.266e-14
53.Fisher-exact testUP00077_2Srf_secondarytop 3760 seqs1.768e-169.406e-14
54.Fisher-exact testMA0136.1ELF5top 3760 seqs4.601e-162.448e-13
55.Fisher-exact testMA0144.1Stat3top 3760 seqs4.857e-162.584e-13
56.Fisher-exact testMA0068.1Pax4top 3760 seqs7.759e-164.128e-13
57.Fisher-exact testUP00035_2Hic1_secondarytop 3760 seqs1.522e-158.099e-13
58.Fisher-exact testMA0156.1FEVtop 3760 seqs3.58e-151.905e-12
59.Fisher-exact testMA0087.1Sox5top 3760 seqs6.494e-153.455e-12
60.Fisher-exact testUP00042_2Gm397_secondarytop 3760 seqs2.268e-141.207e-11
61.Fisher-exact testUP00086_1Irf3_primarytop 3760 seqs2.775e-141.477e-11
62.Fisher-exact testMA0042.1FOXI1top 3760 seqs5.157e-142.743e-11
63.Fisher-exact testUP00073_2Foxa2_secondarytop 3760 seqs6.588e-143.505e-11
64.Fisher-exact testUP00023_1Sox30_primarytop 3760 seqs1.005e-135.346e-11
65.Fisher-exact testMA0137.2STAT1top 3760 seqs2.088e-131.111e-10
66.Fisher-exact testMA0019.1Ddit3::Cebpatop 3760 seqs4.788e-132.547e-10
67.Fisher-exact testMA0080.2SPI1top 3760 seqs7.59e-134.038e-10
68.Fisher-exact testMA0164.1Nr2e3top 3760 seqs1.133e-126.027e-10
69.Fisher-exact testUP00075_1Sox15_primarytop 3760 seqs1.187e-126.313e-10
70.Fisher-exact testUP00007_1Egr1_primarytop 3760 seqs2.602e-121.384e-09
71.Fisher-exact testMA0033.1FOXL1top 3760 seqs3.108e-121.654e-09
72.Fisher-exact testUP00051_1Sox8_primarytop 3760 seqs4.1e-122.181e-09
73.Fisher-exact testUP00064_1Sox18_primarytop 3760 seqs7.304e-123.886e-09
74.Fisher-exact testMA0105.1NFKB1top 3760 seqs8.463e-124.502e-09
75.Fisher-exact testUP00006_2Zic3_secondarytop 3760 seqs8.709e-124.633e-09
76.Fisher-exact testMA0104.2Mycntop 3760 seqs3.071e-111.634e-08
77.Fisher-exact testUP00041_1Foxj1_primarytop 3760 seqs3.957e-112.105e-08
78.Fisher-exact testUP00060_1Max_primarytop 3760 seqs5.121e-112.724e-08
79.Fisher-exact testUP00408_1Gabpa_primarytop 3760 seqs9.574e-115.093e-08
80.Fisher-exact testUP00255_1Dbx1_3486.1top 3760 seqs1.699e-109.038e-08
81.Fisher-exact testUP00071_1Sox21_primarytop 3760 seqs1.845e-109.814e-08
82.Fisher-exact testMA0055.1Myftop 3760 seqs1.885e-101.003e-07
83.Fisher-exact testUP00129_1Pou3f1_3819.1top 3760 seqs2.057e-101.094e-07
84.Fisher-exact testMA0030.1FOXF2top 3760 seqs2.902e-101.544e-07
85.Fisher-exact testUP00094_2Zfp128_secondarytop 3760 seqs4.91e-102.612e-07
86.Fisher-exact testMA0152.1NFATC2top 3760 seqs1.017e-095.409e-07
87.Fisher-exact testUP00102_2Zic1_secondarytop 3760 seqs1.136e-096.042e-07
88.Fisher-exact testMA0116.1Zfp423top 3760 seqs1.333e-097.09e-07
89.Fisher-exact testUP00016_1Sry_primarytop 3760 seqs1.681e-098.943e-07
90.Fisher-exact testUP00254_1Pou2f1_3081.2top 3760 seqs1.905e-091.013e-06
91.Fisher-exact testMA0052.1MEF2Atop 3760 seqs4.244e-092.258e-06
92.Fisher-exact testUP00244_1Tlx2_3498.2top 3760 seqs4.295e-092.285e-06
93.Fisher-exact testMA0058.1MAXtop 3760 seqs4.352e-092.315e-06
94.Fisher-exact testUP00022_1Zfp740_primarytop 3760 seqs4.53e-092.41e-06
95.Fisher-exact testUP00165_1Titf1_1722.2top 3760 seqs4.601e-092.448e-06
96.Fisher-exact testUP00039_2Foxj3_secondarytop 3760 seqs6.728e-093.579e-06
97.Fisher-exact testUP00057_2Zic2_secondarytop 3760 seqs7.506e-093.993e-06
98.Fisher-exact testUP00158_1Pou1f1_3818.1top 3760 seqs8.454e-094.497e-06
99.Fisher-exact testMA0077.1SOX9top 3760 seqs9.395e-094.998e-06
100.Fisher-exact testUP00091_1Sox5_primarytop 3760 seqs9.969e-095.304e-06
101.Fisher-exact testUP00036_2Myf6_secondarytop 3760 seqs1.501e-087.984e-06
102.Fisher-exact testUP00105_1Pou3f4_3773.1top 3760 seqs2.1e-081.117e-05
103.Fisher-exact testMA0050.1IRF1top 3760 seqs2.231e-081.187e-05
104.Fisher-exact testUP00065_1Zfp161_primarytop 3760 seqs2.751e-081.464e-05
105.Fisher-exact testMA0259.1HIF1A::ARNTtop 3760 seqs2.869e-081.526e-05
106.Fisher-exact testMA0157.1FOXO3top 3760 seqs3.457e-081.839e-05
107.Fisher-exact testUP00149_1Phox2b_3948.1top 3760 seqs3.88e-082.064e-05
108.Fisher-exact testUP00028_2Tcfap2e_secondarytop 3760 seqs4.263e-082.268e-05
109.Fisher-exact testMA0090.1TEAD1top 3760 seqs4.405e-082.343e-05
110.Fisher-exact testMA0088.1znf143top 3760 seqs5.77e-083.07e-05
111.Fisher-exact testUP00088_1Plagl1_primarytop 3760 seqs7.356e-083.913e-05
112.Fisher-exact testUP00002_2Sp4_secondarytop 3760 seqs7.885e-084.195e-05
113.Fisher-exact testMA0081.1SPIBtop 3760 seqs9.636e-085.126e-05
114.Fisher-exact testUP00004_2Sox14_secondarytop 3760 seqs1.206e-076.418e-05
115.Fisher-exact testMA0160.1NR4A2top 3760 seqs1.33e-077.076e-05
116.Fisher-exact testMA0047.1Foxa2top 3760 seqs1.343e-077.147e-05
117.Fisher-exact testUP00406_1Spdef_primarytop 3760 seqs1.657e-078.815e-05
118.Fisher-exact testMA0078.1Sox17top 3760 seqs1.751e-079.317e-05
119.Fisher-exact testUP00118_1Pou4f3_2791.1top 3760 seqs2.079e-070.0001106
120.Fisher-exact testUP00047_2Zbtb7b_secondarytop 3760 seqs2.799e-070.0001489
121.Fisher-exact testMA0102.1Cebpatop 3760 seqs3.19e-070.0001697
122.Fisher-exact testUP00249_1Nkx2-5_3436.1top 3760 seqs4.004e-070.000213
123.Fisher-exact testUP00029_2Tbp_secondarytop 3760 seqs6.384e-070.0003396
124.Fisher-exact testUP00172_1Prop1_3949.1top 3760 seqs7.064e-070.0003758
125.Fisher-exact testUP00046_1Tcfe2a_primarytop 3760 seqs1.042e-060.000554
126.Fisher-exact testMA0002.2RUNX1top 3760 seqs1.235e-060.000657
127.Fisher-exact testMA0108.1TBPtop 3760 seqs1.308e-060.0006958
128.Fisher-exact testUP00050_1Bhlhb2_primarytop 3760 seqs1.312e-060.0006977
129.Fisher-exact testMA0102.2CEBPAtop 3760 seqs1.447e-060.0007696
130.Fisher-exact testMA0070.1PBX1top 3760 seqs1.613e-060.000858