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/cMyc.ame_out --verbose 1 --fix-partition 3422 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_cMyc_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 3422.

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 testMA0093.1USF1top 3422 seqs7.217e-2083.84e-205
2.Fisher-exact testMA0004.1Arnttop 3422 seqs7.217e-2083.84e-205
3.Fisher-exact testMA0104.1Mycntop 3422 seqs7.217e-2083.84e-205
4.Fisher-exact testMA0104.2Mycntop 3422 seqs4.478e-1882.383e-185
5.Fisher-exact testUP00060_1Max_primarytop 3422 seqs4.6e-1782.447e-175
6.Fisher-exact testMA0147.1Myctop 3422 seqs1.199e-1776.38e-175
7.Fisher-exact testMA0059.1MYC::MAXtop 3422 seqs5.3e-1652.819e-162
8.Fisher-exact testMA0058.1MAXtop 3422 seqs8.572e-1464.56e-143
9.Fisher-exact testUP00050_2Bhlhb2_secondarytop 3422 seqs2.371e-641.261e-61
10.Fisher-exact testUP00015_1Ehf_primarytop 3422 seqs3.336e-611.775e-58
11.Fisher-exact testUP00407_1Elf3_primarytop 3422 seqs1.383e-607.359e-58
12.Fisher-exact testMA0259.1HIF1A::ARNTtop 3422 seqs1.835e-589.764e-56
13.Fisher-exact testMA0039.2Klf4top 3422 seqs4.393e-572.337e-54
14.Fisher-exact testMA0149.1EWSR1-FLI1top 3422 seqs2.4e-551.277e-52
15.Fisher-exact testUP00093_1Klf7_primarytop 3422 seqs3.959e-552.106e-52
16.Fisher-exact testUP00024_1Glis2_primarytop 3422 seqs4.331e-552.304e-52
17.Fisher-exact testUP00047_1Zbtb7b_primarytop 3422 seqs1.249e-536.646e-51
18.Fisher-exact testUP00050_1Bhlhb2_primarytop 3422 seqs1.185e-526.304e-50
19.Fisher-exact testUP00021_2Zfp281_secondarytop 3422 seqs1.734e-529.223e-50
20.Fisher-exact testUP00022_2Zfp740_secondarytop 3422 seqs2.616e-501.391e-47
21.Fisher-exact testMA0156.1FEVtop 3422 seqs3.386e-471.801e-44
22.Fisher-exact testUP00408_1Gabpa_primarytop 3422 seqs8.538e-444.542e-41
23.Fisher-exact testUP00099_2Ascl2_secondarytop 3422 seqs4.279e-422.276e-39
24.Fisher-exact testMA0062.2GABPAtop 3422 seqs7.782e-414.14e-38
25.Fisher-exact testMA0136.1ELF5top 3422 seqs5.59e-392.974e-36
26.Fisher-exact testMA0073.1RREB1top 3422 seqs7.195e-373.828e-34
27.Fisher-exact testUP00097_2Mtf1_secondarytop 3422 seqs9.036e-364.807e-33
28.Fisher-exact testUP00002_1Sp4_primarytop 3422 seqs1.631e-328.674e-30
29.Fisher-exact testUP00000_2Smad3_secondarytop 3422 seqs5.088e-312.707e-28
30.Fisher-exact testUP00077_2Srf_secondarytop 3422 seqs1.31e-306.969e-28
31.Fisher-exact testUP00037_1Zfp105_primarytop 3422 seqs1.938e-301.031e-27
32.Fisher-exact testMA0079.2SP1top 3422 seqs2.111e-301.123e-27
33.Fisher-exact testUP00033_2Zfp410_secondarytop 3422 seqs2.122e-301.129e-27
34.Fisher-exact testUP00085_1Sfpi1_primarytop 3422 seqs2.611e-301.389e-27
35.Fisher-exact testUP00406_1Spdef_primarytop 3422 seqs9.734e-305.178e-27
36.Fisher-exact testUP00046_1Tcfe2a_primarytop 3422 seqs6.909e-273.676e-24
37.Fisher-exact testMA0062.1GABPAtop 3422 seqs2.967e-261.579e-23
38.Fisher-exact testMA0076.1ELK4top 3422 seqs5.254e-262.795e-23
39.Fisher-exact testUP00088_2Plagl1_secondarytop 3422 seqs7.389e-263.931e-23
40.Fisher-exact testUP00408_2Gabpa_secondarytop 3422 seqs9.517e-265.063e-23
41.Fisher-exact testUP00043_2Bcl6b_secondarytop 3422 seqs1.295e-256.89e-23
42.Fisher-exact testMA0039.1Klf4top 3422 seqs3.973e-252.114e-22
43.Fisher-exact testUP00021_1Zfp281_primarytop 3422 seqs9.269e-254.931e-22
44.Fisher-exact testMA0162.1Egr1top 3422 seqs1.203e-246.402e-22
45.Fisher-exact testMA0105.1NFKB1top 3422 seqs3.792e-242.017e-21
46.Fisher-exact testUP00103_1Jundm2_primarytop 3422 seqs9.62e-245.118e-21
47.Fisher-exact testUP00096_2Sox13_secondarytop 3422 seqs1.922e-221.022e-19
48.Fisher-exact testUP00060_2Max_secondarytop 3422 seqs4.726e-212.514e-18
49.Fisher-exact testUP00061_1Foxl1_primarytop 3422 seqs5.809e-213.09e-18
50.Fisher-exact testMA0100.1Mybtop 3422 seqs6.523e-203.47e-17
51.Fisher-exact testUP00020_1Atf1_primarytop 3422 seqs7.734e-204.115e-17
52.Fisher-exact testUP00088_1Plagl1_primarytop 3422 seqs2.124e-191.13e-16
53.Fisher-exact testMA0137.1STAT1top 3422 seqs5.6e-192.979e-16
54.Fisher-exact testMA0152.1NFATC2top 3422 seqs1.136e-186.043e-16
55.Fisher-exact testUP00407_2Elf3_secondarytop 3422 seqs1.279e-186.805e-16
56.Fisher-exact testMA0116.1Zfp423top 3422 seqs2.5e-181.33e-15
57.Fisher-exact testUP00030_1Sox11_primarytop 3422 seqs2.997e-181.594e-15
58.Fisher-exact testUP00035_2Hic1_secondarytop 3422 seqs8.862e-184.715e-15
59.Fisher-exact testUP00028_2Tcfap2e_secondarytop 3422 seqs1.308e-176.957e-15
60.Fisher-exact testMA0137.2STAT1top 3422 seqs3.48e-171.852e-14
61.Fisher-exact testUP00061_2Foxl1_secondarytop 3422 seqs7.543e-174.013e-14
62.Fisher-exact testUP00062_1Sox4_primarytop 3422 seqs1.246e-166.627e-14
63.Fisher-exact testUP00073_1Foxa2_primarytop 3422 seqs3.206e-161.706e-13
64.Fisher-exact testUP00025_1Foxk1_primarytop 3422 seqs6.348e-163.377e-13
65.Fisher-exact testUP00029_1Tbp_primarytop 3422 seqs7.574e-164.029e-13
66.Fisher-exact testMA0028.1ELK1top 3422 seqs1.06e-155.642e-13
67.Fisher-exact testMA0050.1IRF1top 3422 seqs1.375e-147.316e-12
68.Fisher-exact testUP00039_1Foxj3_primarytop 3422 seqs5.87e-143.123e-11
69.Fisher-exact testMA0144.1Stat3top 3422 seqs6.302e-143.353e-11
70.Fisher-exact testMA0081.1SPIBtop 3422 seqs6.473e-143.444e-11
71.Fisher-exact testMA0041.1Foxd3top 3422 seqs7.093e-143.773e-11
72.Fisher-exact testMA0080.1SPI1top 3422 seqs1.335e-137.103e-11
73.Fisher-exact testMA0098.1ETS1top 3422 seqs1.335e-137.103e-11
74.Fisher-exact testUP00065_1Zfp161_primarytop 3422 seqs2.302e-131.225e-10
75.Fisher-exact testMA0088.1znf143top 3422 seqs1.154e-126.14e-10
76.Fisher-exact testUP00101_2Sox12_secondarytop 3422 seqs3.719e-121.979e-09
77.Fisher-exact testMA0025.1NFIL3top 3422 seqs4.103e-122.183e-09
78.Fisher-exact testUP00244_1Tlx2_3498.2top 3422 seqs7.262e-123.863e-09
79.Fisher-exact testMA0042.1FOXI1top 3422 seqs8.87e-124.719e-09
80.Fisher-exact testUP00041_1Foxj1_primarytop 3422 seqs1.03e-115.482e-09
81.Fisher-exact testMA0119.1TLX1::NFICtop 3422 seqs4.921e-112.618e-08
82.Fisher-exact testMA0055.1Myftop 3422 seqs5.391e-112.868e-08
83.Fisher-exact testMA0080.2SPI1top 3422 seqs1.594e-108.482e-08
84.Fisher-exact testUP00035_1Hic1_primarytop 3422 seqs1.701e-109.048e-08
85.Fisher-exact testUP00042_2Gm397_secondarytop 3422 seqs2.187e-101.163e-07
86.Fisher-exact testUP00092_2Myb_secondarytop 3422 seqs2.5e-101.33e-07
87.Fisher-exact testUP00049_2Sp100_secondarytop 3422 seqs3.112e-101.656e-07
88.Fisher-exact testUP00087_1Tcfap2c_primarytop 3422 seqs5.856e-103.115e-07
89.Fisher-exact testUP00002_2Sp4_secondarytop 3422 seqs7.452e-103.964e-07
90.Fisher-exact testUP00255_1Dbx1_3486.1top 3422 seqs9.747e-105.185e-07
91.Fisher-exact testUP00179_1Pou2f3_3986.2top 3422 seqs1.37e-097.288e-07
92.Fisher-exact testUP00191_1Pou2f2_3748.1top 3422 seqs1.56e-098.297e-07
93.Fisher-exact testMA0148.1FOXA1top 3422 seqs1.651e-098.782e-07
94.Fisher-exact testUP00057_1Zic2_primarytop 3422 seqs1.668e-098.875e-07
95.Fisher-exact testMA0030.1FOXF2top 3422 seqs1.785e-099.498e-07
96.Fisher-exact testMA0079.1SP1top 3422 seqs1.929e-091.026e-06
97.Fisher-exact testUP00047_2Zbtb7b_secondarytop 3422 seqs2.008e-091.068e-06
98.Fisher-exact testUP00007_1Egr1_primarytop 3422 seqs2.277e-091.211e-06
99.Fisher-exact testUP00005_1Tcfap2a_primarytop 3422 seqs2.713e-091.443e-06
100.Fisher-exact testMA0154.1EBF1top 3422 seqs4.041e-092.15e-06
101.Fisher-exact testUP00010_1Tcfap2b_primarytop 3422 seqs4.344e-092.311e-06
102.Fisher-exact testMA0061.1NF-kappaBtop 3422 seqs4.365e-092.322e-06
103.Fisher-exact testMA0130.1ZNF354Ctop 3422 seqs4.747e-092.525e-06
104.Fisher-exact testMA0068.1Pax4top 3422 seqs1.802e-089.589e-06
105.Fisher-exact testMA0002.2RUNX1top 3422 seqs3.757e-081.999e-05
106.Fisher-exact testMA0060.1NFYAtop 3422 seqs3.959e-082.106e-05
107.Fisher-exact testUP00081_2Mybl1_secondarytop 3422 seqs4.103e-082.183e-05
108.Fisher-exact testMA0043.1HLFtop 3422 seqs4.918e-082.616e-05
109.Fisher-exact testUP00006_1Zic3_primarytop 3422 seqs5.282e-082.81e-05
110.Fisher-exact testUP00188_1Lmx1a_2238.2top 3422 seqs6.372e-083.39e-05
111.Fisher-exact testUP00102_1Zic1_primarytop 3422 seqs7.925e-084.216e-05
112.Fisher-exact testUP00099_1Ascl2_primarytop 3422 seqs8.313e-084.422e-05
113.Fisher-exact testUP00086_1Irf3_primarytop 3422 seqs1.757e-079.345e-05
114.Fisher-exact testUP00073_2Foxa2_secondarytop 3422 seqs2.83e-070.0001505
115.Fisher-exact testUP00024_2Glis2_secondarytop 3422 seqs3.8e-070.0002021
116.Fisher-exact testMA0157.1FOXO3top 3422 seqs4.427e-070.0002355
117.Fisher-exact testUP00097_1Mtf1_primarytop 3422 seqs7.159e-070.0003808
118.Fisher-exact testMA0047.2Foxa2top 3422 seqs7.813e-070.0004156
119.Fisher-exact testMA0051.1IRF2top 3422 seqs7.893e-070.0004198
120.Fisher-exact testUP00076_2Rfxdc2_secondarytop 3422 seqs7.987e-070.0004248
121.Fisher-exact testUP00070_2Gcm1_secondarytop 3422 seqs8.839e-070.0004701
122.Fisher-exact testUP00231_1Nkx2-2_2823.1top 3422 seqs9.972e-070.0005304
123.Fisher-exact testUP00169_1Lmx1b_3433.2top 3422 seqs1.323e-060.0007036
124.Fisher-exact testUP00168_1Hoxd8_2644.1top 3422 seqs1.462e-060.0007773