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/nMyc.ame_out --verbose 1 --fix-partition 7182 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_nMyc_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 7182.

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 7182 seqs8.472e-2894.507e-286
2.Fisher-exact testMA0004.1Arnttop 7182 seqs8.472e-2894.507e-286
3.Fisher-exact testMA0104.1Mycntop 7182 seqs8.472e-2894.507e-286
4.Fisher-exact testMA0104.2Mycntop 7182 seqs6.132e-2513.262e-248
5.Fisher-exact testMA0147.1Myctop 7182 seqs2.029e-2381.08e-235
6.Fisher-exact testUP00060_1Max_primarytop 7182 seqs1.632e-2198.683e-217
7.Fisher-exact testMA0059.1MYC::MAXtop 7182 seqs8.765e-2114.663e-208
8.Fisher-exact testMA0058.1MAXtop 7182 seqs9.446e-1955.025e-192
9.Fisher-exact testUP00047_1Zbtb7b_primarytop 7182 seqs5.076e-1272.7e-124
10.Fisher-exact testUP00021_2Zfp281_secondarytop 7182 seqs1.27e-1176.757e-115
11.Fisher-exact testUP00024_1Glis2_primarytop 7182 seqs6.74e-1133.586e-110
12.Fisher-exact testUP00022_2Zfp740_secondarytop 7182 seqs1.798e-1059.564e-103
13.Fisher-exact testMA0149.1EWSR1-FLI1top 7182 seqs2.629e-1041.399e-101
14.Fisher-exact testUP00093_1Klf7_primarytop 7182 seqs1.198e-986.374e-96
15.Fisher-exact testUP00050_2Bhlhb2_secondarytop 7182 seqs1.115e-965.931e-94
16.Fisher-exact testUP00015_1Ehf_primarytop 7182 seqs1.44e-927.659e-90
17.Fisher-exact testMA0039.2Klf4top 7182 seqs3.668e-911.951e-88
18.Fisher-exact testMA0259.1HIF1A::ARNTtop 7182 seqs3.201e-871.703e-84
19.Fisher-exact testUP00407_1Elf3_primarytop 7182 seqs1.658e-828.82e-80
20.Fisher-exact testUP00099_2Ascl2_secondarytop 7182 seqs8.85e-824.708e-79
21.Fisher-exact testMA0073.1RREB1top 7182 seqs3.206e-801.706e-77
22.Fisher-exact testUP00050_1Bhlhb2_primarytop 7182 seqs4.455e-792.37e-76
23.Fisher-exact testMA0062.2GABPAtop 7182 seqs2.594e-681.38e-65
24.Fisher-exact testUP00088_2Plagl1_secondarytop 7182 seqs3.021e-651.607e-62
25.Fisher-exact testUP00408_2Gabpa_secondarytop 7182 seqs9.462e-645.034e-61
26.Fisher-exact testUP00000_2Smad3_secondarytop 7182 seqs1.007e-635.357e-61
27.Fisher-exact testMA0156.1FEVtop 7182 seqs5.959e-633.17e-60
28.Fisher-exact testUP00002_1Sp4_primarytop 7182 seqs1.334e-627.095e-60
29.Fisher-exact testMA0162.1Egr1top 7182 seqs6.82e-623.628e-59
30.Fisher-exact testUP00033_2Zfp410_secondarytop 7182 seqs1.508e-608.021e-58
31.Fisher-exact testUP00077_2Srf_secondarytop 7182 seqs2.938e-591.563e-56
32.Fisher-exact testUP00097_2Mtf1_secondarytop 7182 seqs2.22e-581.181e-55
33.Fisher-exact testMA0136.1ELF5top 7182 seqs1.079e-575.741e-55
34.Fisher-exact testUP00408_1Gabpa_primarytop 7182 seqs5.243e-572.789e-54
35.Fisher-exact testMA0079.2SP1top 7182 seqs7.242e-533.853e-50
36.Fisher-exact testUP00037_1Zfp105_primarytop 7182 seqs7.762e-534.129e-50
37.Fisher-exact testUP00085_1Sfpi1_primarytop 7182 seqs8.988e-524.782e-49
38.Fisher-exact testUP00406_1Spdef_primarytop 7182 seqs3.484e-491.853e-46
39.Fisher-exact testMA0062.1GABPAtop 7182 seqs1.238e-486.587e-46
40.Fisher-exact testMA0105.1NFKB1top 7182 seqs2.781e-481.479e-45
41.Fisher-exact testUP00021_1Zfp281_primarytop 7182 seqs7.521e-464.001e-43
42.Fisher-exact testUP00096_2Sox13_secondarytop 7182 seqs1.097e-435.838e-41
43.Fisher-exact testMA0039.1Klf4top 7182 seqs5.383e-432.864e-40
44.Fisher-exact testUP00103_1Jundm2_primarytop 7182 seqs3.292e-411.751e-38
45.Fisher-exact testMA0076.1ELK4top 7182 seqs1.468e-407.809e-38
46.Fisher-exact testUP00061_1Foxl1_primarytop 7182 seqs4.984e-392.651e-36
47.Fisher-exact testUP00043_2Bcl6b_secondarytop 7182 seqs5.616e-392.988e-36
48.Fisher-exact testUP00065_1Zfp161_primarytop 7182 seqs1.475e-387.846e-36
49.Fisher-exact testUP00046_1Tcfe2a_primarytop 7182 seqs2.743e-381.459e-35
50.Fisher-exact testUP00039_1Foxj3_primarytop 7182 seqs5.349e-372.846e-34
51.Fisher-exact testUP00060_2Max_secondarytop 7182 seqs2.389e-351.271e-32
52.Fisher-exact testUP00020_1Atf1_primarytop 7182 seqs1.132e-346.025e-32
53.Fisher-exact testMA0041.1Foxd3top 7182 seqs3.729e-341.984e-31
54.Fisher-exact testMA0116.1Zfp423top 7182 seqs1.537e-338.179e-31
55.Fisher-exact testUP00030_1Sox11_primarytop 7182 seqs3.423e-331.821e-30
56.Fisher-exact testUP00062_1Sox4_primarytop 7182 seqs1.581e-328.412e-30
57.Fisher-exact testMA0144.1Stat3top 7182 seqs1.93e-321.027e-29
58.Fisher-exact testUP00035_2Hic1_secondarytop 7182 seqs2.027e-321.078e-29
59.Fisher-exact testMA0068.1Pax4top 7182 seqs4.332e-322.304e-29
60.Fisher-exact testUP00073_1Foxa2_primarytop 7182 seqs6.185e-313.29e-28
61.Fisher-exact testMA0152.1NFATC2top 7182 seqs3.258e-301.733e-27
62.Fisher-exact testUP00088_1Plagl1_primarytop 7182 seqs3.371e-301.793e-27
63.Fisher-exact testUP00407_2Elf3_secondarytop 7182 seqs1.282e-296.819e-27
64.Fisher-exact testMA0088.1znf143top 7182 seqs2.034e-271.082e-24
65.Fisher-exact testMA0100.1Mybtop 7182 seqs3.097e-271.648e-24
66.Fisher-exact testMA0137.1STAT1top 7182 seqs4.183e-272.225e-24
67.Fisher-exact testUP00025_1Foxk1_primarytop 7182 seqs1.266e-266.734e-24
68.Fisher-exact testMA0042.1FOXI1top 7182 seqs1.786e-269.499e-24
69.Fisher-exact testMA0055.1Myftop 7182 seqs1.923e-261.023e-23
70.Fisher-exact testUP00061_2Foxl1_secondarytop 7182 seqs3.185e-261.694e-23
71.Fisher-exact testMA0080.2SPI1top 7182 seqs5.037e-262.68e-23
72.Fisher-exact testMA0030.1FOXF2top 7182 seqs5.835e-253.104e-22
73.Fisher-exact testMA0137.2STAT1top 7182 seqs1.735e-249.233e-22
74.Fisher-exact testMA0081.1SPIBtop 7182 seqs2.04e-241.085e-21
75.Fisher-exact testUP00028_2Tcfap2e_secondarytop 7182 seqs1.253e-236.667e-21
76.Fisher-exact testUP00029_1Tbp_primarytop 7182 seqs4.782e-232.544e-20
77.Fisher-exact testUP00042_2Gm397_secondarytop 7182 seqs5.018e-222.67e-19
78.Fisher-exact testUP00041_1Foxj1_primarytop 7182 seqs8.074e-224.295e-19
79.Fisher-exact testMA0079.1SP1top 7182 seqs1.202e-216.396e-19
80.Fisher-exact testUP00002_2Sp4_secondarytop 7182 seqs2.265e-211.205e-18
81.Fisher-exact testUP00007_1Egr1_primarytop 7182 seqs1.031e-205.487e-18
82.Fisher-exact testUP00099_1Ascl2_primarytop 7182 seqs1.109e-205.9e-18
83.Fisher-exact testMA0080.1SPI1top 7182 seqs1.637e-208.707e-18
84.Fisher-exact testMA0098.1ETS1top 7182 seqs1.637e-208.707e-18
85.Fisher-exact testUP00047_2Zbtb7b_secondarytop 7182 seqs4.159e-202.212e-17
86.Fisher-exact testMA0148.1FOXA1top 7182 seqs1.909e-191.016e-16
87.Fisher-exact testUP00081_2Mybl1_secondarytop 7182 seqs2.892e-191.538e-16
88.Fisher-exact testMA0157.1FOXO3top 7182 seqs4.152e-192.209e-16
89.Fisher-exact testUP00244_1Tlx2_3498.2top 7182 seqs3.024e-171.609e-14
90.Fisher-exact testUP00049_2Sp100_secondarytop 7182 seqs3.622e-171.927e-14
91.Fisher-exact testMA0014.1Pax5top 7182 seqs3.998e-172.127e-14
92.Fisher-exact testMA0154.1EBF1top 7182 seqs2.02e-161.075e-13
93.Fisher-exact testMA0061.1NF-kappaBtop 7182 seqs2.482e-161.321e-13
94.Fisher-exact testUP00191_1Pou2f2_3748.1top 7182 seqs2.761e-161.469e-13
95.Fisher-exact testMA0028.1ELK1top 7182 seqs2.903e-161.545e-13
96.Fisher-exact testMA0164.1Nr2e3top 7182 seqs4.024e-162.141e-13
97.Fisher-exact testUP00101_2Sox12_secondarytop 7182 seqs4.677e-162.488e-13
98.Fisher-exact testUP00255_1Dbx1_3486.1top 7182 seqs1.017e-155.41e-13
99.Fisher-exact testUP00057_1Zic2_primarytop 7182 seqs3.145e-151.673e-12
100.Fisher-exact testMA0050.1IRF1top 7182 seqs3.18e-151.692e-12
101.Fisher-exact testUP00066_1Hnf4a_primarytop 7182 seqs4.134e-152.199e-12
102.Fisher-exact testMA0025.1NFIL3top 7182 seqs9.02e-154.799e-12
103.Fisher-exact testMA0142.1Pou5f1top 7182 seqs1.814e-149.648e-12
104.Fisher-exact testMA0084.1SRYtop 7182 seqs3.059e-141.627e-11
105.Fisher-exact testUP00035_1Hic1_primarytop 7182 seqs4.372e-142.326e-11
106.Fisher-exact testUP00121_1Hoxd10_2368.2top 7182 seqs1.11e-135.904e-11
107.Fisher-exact testUP00101_1Sox12_primarytop 7182 seqs1.296e-136.896e-11
108.Fisher-exact testUP00010_1Tcfap2b_primarytop 7182 seqs2.049e-131.09e-10
109.Fisher-exact testMA0114.1HNF4Atop 7182 seqs2.117e-131.126e-10
110.Fisher-exact testMA0119.1TLX1::NFICtop 7182 seqs2.928e-131.558e-10
111.Fisher-exact testUP00179_1Pou2f3_3986.2top 7182 seqs3e-131.596e-10
112.Fisher-exact testUP00188_1Lmx1a_2238.2top 7182 seqs4.831e-132.57e-10
113.Fisher-exact testUP00006_1Zic3_primarytop 7182 seqs5.585e-132.971e-10
114.Fisher-exact testUP00087_1Tcfap2c_primarytop 7182 seqs1.5e-127.979e-10
115.Fisher-exact testMA0130.1ZNF354Ctop 7182 seqs2.591e-121.378e-09
116.Fisher-exact testUP00180_1Hoxd13_2356.1top 7182 seqs2.772e-121.474e-09
117.Fisher-exact testUP00086_1Irf3_primarytop 7182 seqs3.789e-122.016e-09
118.Fisher-exact testMA0056.1MZF1_1-4top 7182 seqs6.777e-123.606e-09
119.Fisher-exact testUP00092_2Myb_secondarytop 7182 seqs8.021e-124.267e-09
120.Fisher-exact testMA0043.1HLFtop 7182 seqs8.563e-124.555e-09
121.Fisher-exact testUP00036_2Myf6_secondarytop 7182 seqs9.085e-124.833e-09
122.Fisher-exact testMA0067.1Pax2top 7182 seqs9.7e-125.16e-09
123.Fisher-exact testUP00026_1Zscan4_primarytop 7182 seqs1.395e-117.423e-09
124.Fisher-exact testUP00231_1Nkx2-2_2823.1top 7182 seqs2.035e-111.083e-08
125.Fisher-exact testMA0143.1Sox2top 7182 seqs4.113e-112.188e-08
126.Fisher-exact testMA0040.1Foxq1top 7182 seqs7.477e-113.978e-08
127.Fisher-exact testUP00102_1Zic1_primarytop 7182 seqs1.626e-108.649e-08
128.Fisher-exact testUP00087_2Tcfap2c_secondarytop 7182 seqs2.499e-101.329e-07
129.Fisher-exact testUP00071_1Sox21_primarytop 7182 seqs9.157e-104.872e-07
130.Fisher-exact testMA0138.1RESTtop 7182 seqs2.515e-091.338e-06
131.Fisher-exact testUP00168_1Hoxd8_2644.1top 7182 seqs2.591e-091.379e-06
132.Fisher-exact testUP00034_1Sox7_primarytop 7182 seqs3.242e-091.725e-06
133.Fisher-exact testMA0047.2Foxa2top 7182 seqs4.311e-092.294e-06
134.Fisher-exact testMA0102.2CEBPAtop 7182 seqs5.586e-092.971e-06
135.Fisher-exact testUP00243_1Isx_3445.1top 7182 seqs6.013e-093.199e-06
136.Fisher-exact testUP00265_1Pitx3_3497.2top 7182 seqs6.376e-093.392e-06
137.Fisher-exact testUP00158_1Pou1f1_3818.1top 7182 seqs6.958e-093.702e-06
138.Fisher-exact testUP00105_1Pou3f4_3773.1top 7182 seqs8.751e-094.656e-06
139.Fisher-exact testMA0052.1MEF2Atop 7182 seqs1.128e-086e-06
140.Fisher-exact testUP00169_1Lmx1b_3433.2top 7182 seqs1.237e-086.581e-06
141.Fisher-exact testUP00005_1Tcfap2a_primarytop 7182 seqs1.515e-088.06e-06
142.Fisher-exact testUP00074_1Isgf3g_primarytop 7182 seqs1.566e-088.329e-06
143.Fisher-exact testUP00051_1Sox8_primarytop 7182 seqs4.204e-082.236e-05
144.Fisher-exact testMA0048.1NHLH1top 7182 seqs4.268e-082.271e-05
145.Fisher-exact testMA0135.1Lhx3top 7182 seqs4.884e-082.598e-05
146.Fisher-exact testUP00254_1Pou2f1_3081.2top 7182 seqs6.886e-083.663e-05
147.Fisher-exact testUP00042_1Gm397_primarytop 7182 seqs9.34e-084.969e-05
148.Fisher-exact testUP00230_1Dlx5_3419.2top 7182 seqs9.519e-085.064e-05
149.Fisher-exact testUP00076_2Rfxdc2_secondarytop 7182 seqs9.659e-085.139e-05
150.Fisher-exact testMA0060.1NFYAtop 7182 seqs1.065e-075.664e-05
151.Fisher-exact testUP00073_2Foxa2_secondarytop 7182 seqs1.341e-077.133e-05
152.Fisher-exact testUP00004_1Sox14_primarytop 7182 seqs1.366e-077.267e-05
153.Fisher-exact testUP00097_1Mtf1_primarytop 7182 seqs1.441e-077.667e-05
154.Fisher-exact testUP00075_1Sox15_primarytop 7182 seqs1.688e-078.977e-05
155.Fisher-exact testUP00220_1Nkx1-1_3856.3top 7182 seqs1.814e-079.652e-05
156.Fisher-exact testMA0031.1FOXD1top 7182 seqs2.548e-070.0001356
157.Fisher-exact testUP00096_1Sox13_primarytop 7182 seqs2.62e-070.0001394
158.Fisher-exact testUP00064_1Sox18_primarytop 7182 seqs2.972e-070.0001581
159.Fisher-exact testUP00217_1Hoxa10_2318.1top 7182 seqs3.078e-070.0001637
160.Fisher-exact testUP00118_1Pou4f3_2791.1top 7182 seqs3.171e-070.0001687
161.Fisher-exact testMA0102.1Cebpatop 7182 seqs3.87e-070.0002059
162.Fisher-exact testUP00033_1Zfp410_primarytop 7182 seqs4.123e-070.0002193
163.Fisher-exact testUP00129_1Pou3f1_3819.1top 7182 seqs4.646e-070.0002471
164.Fisher-exact testMA0046.1HNF1Atop 7182 seqs5.166e-070.0002748
165.Fisher-exact testMA0006.1Arnt::Ahrtop 7182 seqs5.17e-070.000275
166.Fisher-exact testUP00094_2Zfp128_secondarytop 7182 seqs5.293e-070.0002816
167.Fisher-exact testUP00200_2Nkx6-1_2825.2top 7182 seqs5.823e-070.0003097
168.Fisher-exact testUP00165_1Titf1_1722.2top 7182 seqs7.153e-070.0003805
169.Fisher-exact testUP00024_2Glis2_secondarytop 7182 seqs1.126e-060.0005986
170.Fisher-exact testUP00263_1Hoxb8_3780.2top 7182 seqs1.327e-060.0007058
171.Fisher-exact testMA0002.2RUNX1top 7182 seqs1.636e-060.00087
172.Fisher-exact testMA0138.2RESTtop 7182 seqs1.766e-060.0009391