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/STAT3.ame_out --verbose 1 --fix-partition 2546 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_STAT3_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 2546.

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 testMA0137.2STAT1top 2546 seqs1.259e-1226.697e-120
2.Fisher-exact testMA0144.1Stat3top 2546 seqs1.205e-1086.41e-106
3.Fisher-exact testMA0039.2Klf4top 2546 seqs3.278e-631.744e-60
4.Fisher-exact testUP00093_1Klf7_primarytop 2546 seqs3.256e-581.732e-55
5.Fisher-exact testUP00002_1Sp4_primarytop 2546 seqs1.152e-406.127e-38
6.Fisher-exact testUP00099_2Ascl2_secondarytop 2546 seqs7.199e-403.83e-37
7.Fisher-exact testUP00021_2Zfp281_secondarytop 2546 seqs3.576e-391.903e-36
8.Fisher-exact testMA0073.1RREB1top 2546 seqs5.488e-352.92e-32
9.Fisher-exact testMA0149.1EWSR1-FLI1top 2546 seqs2.735e-341.455e-31
10.Fisher-exact testMA0142.1Pou5f1top 2546 seqs2.653e-331.411e-30
11.Fisher-exact testMA0079.2SP1top 2546 seqs7.49e-313.985e-28
12.Fisher-exact testUP00047_1Zbtb7b_primarytop 2546 seqs1.767e-309.399e-28
13.Fisher-exact testUP00000_2Smad3_secondarytop 2546 seqs5.719e-303.043e-27
14.Fisher-exact testMA0143.1Sox2top 2546 seqs1.358e-297.227e-27
15.Fisher-exact testMA0062.2GABPAtop 2546 seqs1.823e-299.699e-27
16.Fisher-exact testUP00021_1Zfp281_primarytop 2546 seqs6.67e-293.548e-26
17.Fisher-exact testUP00022_2Zfp740_secondarytop 2546 seqs9.212e-294.901e-26
18.Fisher-exact testMA0162.1Egr1top 2546 seqs3.273e-281.741e-25
19.Fisher-exact testUP00015_1Ehf_primarytop 2546 seqs3.404e-281.811e-25
20.Fisher-exact testUP00407_1Elf3_primarytop 2546 seqs7.3e-283.884e-25
21.Fisher-exact testUP00033_2Zfp410_secondarytop 2546 seqs1.191e-276.338e-25
22.Fisher-exact testMA0156.1FEVtop 2546 seqs3.166e-261.685e-23
23.Fisher-exact testUP00043_2Bcl6b_secondarytop 2546 seqs1.3e-256.914e-23
24.Fisher-exact testUP00408_2Gabpa_secondarytop 2546 seqs5.451e-242.9e-21
25.Fisher-exact testUP00024_1Glis2_primarytop 2546 seqs9.567e-245.089e-21
26.Fisher-exact testUP00062_1Sox4_primarytop 2546 seqs5.615e-232.987e-20
27.Fisher-exact testUP00191_1Pou2f2_3748.1top 2546 seqs7.356e-223.913e-19
28.Fisher-exact testMA0068.1Pax4top 2546 seqs1.622e-218.63e-19
29.Fisher-exact testUP00030_1Sox11_primarytop 2546 seqs2.37e-211.261e-18
30.Fisher-exact testUP00007_1Egr1_primarytop 2546 seqs7.388e-213.93e-18
31.Fisher-exact testUP00073_1Foxa2_primarytop 2546 seqs2.558e-191.361e-16
32.Fisher-exact testUP00179_1Pou2f3_3986.2top 2546 seqs4.472e-192.379e-16
33.Fisher-exact testMA0079.1SP1top 2546 seqs1.111e-185.91e-16
34.Fisher-exact testMA0062.1GABPAtop 2546 seqs2.425e-181.29e-15
35.Fisher-exact testUP00025_1Foxk1_primarytop 2546 seqs2.713e-181.443e-15
36.Fisher-exact testMA0039.1Klf4top 2546 seqs3.807e-172.025e-14
37.Fisher-exact testUP00061_1Foxl1_primarytop 2546 seqs4.223e-172.247e-14
38.Fisher-exact testUP00043_1Bcl6b_primarytop 2546 seqs2.106e-161.12e-13
39.Fisher-exact testUP00408_1Gabpa_primarytop 2546 seqs6.624e-163.524e-13
40.Fisher-exact testMA0041.1Foxd3top 2546 seqs8.798e-164.681e-13
41.Fisher-exact testUP00077_2Srf_secondarytop 2546 seqs1.461e-157.77e-13
42.Fisher-exact testUP00101_2Sox12_secondarytop 2546 seqs2.354e-151.252e-12
43.Fisher-exact testMA0136.1ELF5top 2546 seqs3.109e-151.654e-12
44.Fisher-exact testUP00061_2Foxl1_secondarytop 2546 seqs3.141e-151.671e-12
45.Fisher-exact testMA0076.1ELK4top 2546 seqs8.879e-154.724e-12
46.Fisher-exact testUP00088_2Plagl1_secondarytop 2546 seqs1.202e-146.397e-12
47.Fisher-exact testUP00022_1Zfp740_primarytop 2546 seqs2.594e-141.38e-11
48.Fisher-exact testMA0157.1FOXO3top 2546 seqs3.959e-142.106e-11
49.Fisher-exact testMA0137.1STAT1top 2546 seqs6.329e-143.367e-11
50.Fisher-exact testUP00097_2Mtf1_secondarytop 2546 seqs6.945e-143.695e-11
51.Fisher-exact testUP00039_1Foxj3_primarytop 2546 seqs8.017e-144.265e-11
52.Fisher-exact testUP00041_1Foxj1_primarytop 2546 seqs1.285e-136.839e-11
53.Fisher-exact testUP00073_2Foxa2_secondarytop 2546 seqs2.521e-131.341e-10
54.Fisher-exact testUP00029_1Tbp_primarytop 2546 seqs2.666e-131.418e-10
55.Fisher-exact testMA0047.2Foxa2top 2546 seqs3.283e-131.747e-10
56.Fisher-exact testUP00088_1Plagl1_primarytop 2546 seqs4.232e-132.251e-10
57.Fisher-exact testMA0004.1Arnttop 2546 seqs5.15e-132.74e-10
58.Fisher-exact testMA0104.1Mycntop 2546 seqs5.15e-132.74e-10
59.Fisher-exact testMA0093.1USF1top 2546 seqs5.15e-132.74e-10
60.Fisher-exact testUP00096_2Sox13_secondarytop 2546 seqs5.936e-133.158e-10
61.Fisher-exact testUP00406_1Spdef_primarytop 2546 seqs7.474e-133.976e-10
62.Fisher-exact testMA0084.1SRYtop 2546 seqs1.301e-126.924e-10
63.Fisher-exact testMA0141.1Esrrbtop 2546 seqs1.575e-128.378e-10
64.Fisher-exact testUP00057_2Zic2_secondarytop 2546 seqs3.504e-121.864e-09
65.Fisher-exact testMA0148.1FOXA1top 2546 seqs3.624e-121.928e-09
66.Fisher-exact testUP00006_2Zic3_secondarytop 2546 seqs3.665e-121.95e-09
67.Fisher-exact testUP00034_1Sox7_primarytop 2546 seqs9.474e-125.04e-09
68.Fisher-exact testUP00037_1Zfp105_primarytop 2546 seqs5.101e-112.714e-08
69.Fisher-exact testUP00086_1Irf3_primarytop 2546 seqs7.318e-113.893e-08
70.Fisher-exact testMA0105.1NFKB1top 2546 seqs8.496e-114.52e-08
71.Fisher-exact testMA0050.1IRF1top 2546 seqs9.508e-115.058e-08
72.Fisher-exact testMA0080.2SPI1top 2546 seqs1.095e-105.825e-08
73.Fisher-exact testMA0030.1FOXF2top 2546 seqs1.987e-101.057e-07
74.Fisher-exact testUP00102_2Zic1_secondarytop 2546 seqs2.43e-101.293e-07
75.Fisher-exact testUP00035_2Hic1_secondarytop 2546 seqs2.927e-101.557e-07
76.Fisher-exact testMA0160.1NR4A2top 2546 seqs3.613e-101.922e-07
77.Fisher-exact testMA0042.1FOXI1top 2546 seqs5.517e-102.935e-07
78.Fisher-exact testUP00047_2Zbtb7b_secondarytop 2546 seqs1.447e-097.697e-07
79.Fisher-exact testMA0088.1znf143top 2546 seqs1.659e-098.825e-07
80.Fisher-exact testUP00074_1Isgf3g_primarytop 2546 seqs4.242e-092.257e-06
81.Fisher-exact testMA0058.1MAXtop 2546 seqs4.983e-092.651e-06
82.Fisher-exact testUP00042_2Gm397_secondarytop 2546 seqs5.124e-092.726e-06
83.Fisher-exact testMA0164.1Nr2e3top 2546 seqs5.578e-092.968e-06
84.Fisher-exact testUP00227_1Duxl_1286.2top 2546 seqs8.135e-094.328e-06
85.Fisher-exact testMA0055.1Myftop 2546 seqs9.243e-094.917e-06
86.Fisher-exact testUP00075_1Sox15_primarytop 2546 seqs9.832e-095.231e-06
87.Fisher-exact testUP00101_1Sox12_primarytop 2546 seqs1.129e-086.006e-06
88.Fisher-exact testMA0116.1Zfp423top 2546 seqs1.305e-086.945e-06
89.Fisher-exact testUP00051_1Sox8_primarytop 2546 seqs1.427e-087.593e-06
90.Fisher-exact testUP00094_2Zfp128_secondarytop 2546 seqs4.011e-082.134e-05
91.Fisher-exact testUP00099_1Ascl2_primarytop 2546 seqs4.299e-082.287e-05
92.Fisher-exact testUP00255_1Dbx1_3486.1top 2546 seqs8.634e-084.593e-05
93.Fisher-exact testMA0048.1NHLH1top 2546 seqs8.739e-084.649e-05
94.Fisher-exact testUP00050_1Bhlhb2_primarytop 2546 seqs2.232e-070.0001187
95.Fisher-exact testUP00244_1Tlx2_3498.2top 2546 seqs2.988e-070.000159
96.Fisher-exact testUP00054_2Tcf7_secondarytop 2546 seqs3.622e-070.0001927
97.Fisher-exact testUP00035_1Hic1_primarytop 2546 seqs4.97e-070.0002644
98.Fisher-exact testUP00079_1Esrra_primarytop 2546 seqs6.224e-070.000331
99.Fisher-exact testMA0040.1Foxq1top 2546 seqs7.394e-070.0003933
100.Fisher-exact testMA0052.1MEF2Atop 2546 seqs9.66e-070.0005138
101.Fisher-exact testMA0077.1SOX9top 2546 seqs1.136e-060.000604
102.Fisher-exact testMA0102.2CEBPAtop 2546 seqs1.157e-060.0006156
103.Fisher-exact testUP00217_1Hoxa10_2318.1top 2546 seqs1.186e-060.0006308
104.Fisher-exact testUP00231_1Nkx2-2_2823.1top 2546 seqs1.58e-060.0008402
105.Fisher-exact testMA0122.1Nkx3-2top 2546 seqs1.677e-060.0008918