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/Smad1.ame_out --verbose 1 --fix-partition 1126 --bgformat 0 data/chipseq_databases/Chen_ChIP_seq_datasets//mm8_Smad1_ESC_chen-shuffled_w_bg.fasta data/motif_databases/all_vertebrates.meme

Not in partition maximisation mode. Fixing partition at 1126.

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 1126 seqs1.088e-585.788e-56
2.Fisher-exact testMA0143.1Sox2top 1126 seqs3.322e-471.767e-44
3.Fisher-exact testMA0039.2Klf4top 1126 seqs1.99e-281.059e-25
4.Fisher-exact testUP00062_1Sox4_primarytop 1126 seqs1.99e-261.058e-23
5.Fisher-exact testUP00030_1Sox11_primarytop 1126 seqs3.187e-261.696e-23
6.Fisher-exact testUP00191_1Pou2f2_3748.1top 1126 seqs4.43e-242.357e-21
7.Fisher-exact testUP00179_1Pou2f3_3986.2top 1126 seqs4.43e-242.357e-21
8.Fisher-exact testUP00093_1Klf7_primarytop 1126 seqs1.209e-216.432e-19
9.Fisher-exact testMA0079.2SP1top 1126 seqs5.412e-212.879e-18
10.Fisher-exact testUP00102_2Zic1_secondarytop 1126 seqs3.866e-192.057e-16
11.Fisher-exact testUP00006_2Zic3_secondarytop 1126 seqs4.724e-192.513e-16
12.Fisher-exact testUP00057_2Zic2_secondarytop 1126 seqs5.71e-193.038e-16
13.Fisher-exact testUP00099_2Ascl2_secondarytop 1126 seqs8.863e-184.715e-15
14.Fisher-exact testUP00021_1Zfp281_primarytop 1126 seqs8.99e-184.783e-15
15.Fisher-exact testUP00034_1Sox7_primarytop 1126 seqs3.904e-172.077e-14
16.Fisher-exact testUP00023_1Sox30_primarytop 1126 seqs1.032e-165.488e-14
17.Fisher-exact testUP00002_1Sp4_primarytop 1126 seqs7.26e-163.862e-13
18.Fisher-exact testUP00043_2Bcl6b_secondarytop 1126 seqs1.378e-157.331e-13
19.Fisher-exact testMA0073.1RREB1top 1126 seqs1.684e-158.961e-13
20.Fisher-exact testUP00061_1Foxl1_primarytop 1126 seqs1.567e-148.335e-12
21.Fisher-exact testUP00101_2Sox12_secondarytop 1126 seqs7.403e-143.938e-11
22.Fisher-exact testUP00101_1Sox12_primarytop 1126 seqs1.017e-135.413e-11
23.Fisher-exact testUP00004_2Sox14_secondarytop 1126 seqs3.885e-132.067e-10
24.Fisher-exact testMA0162.1Egr1top 1126 seqs8.149e-134.335e-10
25.Fisher-exact testMA0084.1SRYtop 1126 seqs1.291e-126.868e-10
26.Fisher-exact testUP00033_2Zfp410_secondarytop 1126 seqs1.622e-128.627e-10
27.Fisher-exact testMA0079.1SP1top 1126 seqs7.198e-123.829e-09
28.Fisher-exact testUP00000_2Smad3_secondarytop 1126 seqs1.992e-111.06e-08
29.Fisher-exact testMA0062.1GABPAtop 1126 seqs2.117e-111.126e-08
30.Fisher-exact testUP00211_1Pou3f3_3235.2top 1126 seqs2.528e-111.345e-08
31.Fisher-exact testMA0077.1SOX9top 1126 seqs3.384e-111.801e-08
32.Fisher-exact testUP00021_2Zfp281_secondarytop 1126 seqs4.728e-112.515e-08
33.Fisher-exact testUP00096_2Sox13_secondarytop 1126 seqs2.465e-101.311e-07
34.Fisher-exact testUP00061_2Foxl1_secondarytop 1126 seqs2.896e-101.541e-07
35.Fisher-exact testUP00097_2Mtf1_secondarytop 1126 seqs3.045e-101.62e-07
36.Fisher-exact testUP00408_2Gabpa_secondarytop 1126 seqs5.247e-102.791e-07
37.Fisher-exact testUP00047_1Zbtb7b_primarytop 1126 seqs5.27e-102.804e-07
38.Fisher-exact testMA0078.1Sox17top 1126 seqs5.714e-103.04e-07
39.Fisher-exact testMA0042.1FOXI1top 1126 seqs7.271e-103.868e-07
40.Fisher-exact testUP00099_1Ascl2_primarytop 1126 seqs1.459e-097.76e-07
41.Fisher-exact testMA0149.1EWSR1-FLI1top 1126 seqs1.933e-091.029e-06
42.Fisher-exact testUP00073_1Foxa2_primarytop 1126 seqs2.066e-091.099e-06
43.Fisher-exact testUP00042_2Gm397_secondarytop 1126 seqs5.593e-092.975e-06
44.Fisher-exact testMA0060.1NFYAtop 1126 seqs2.039e-081.085e-05
45.Fisher-exact testUP00037_1Zfp105_primarytop 1126 seqs2.073e-081.103e-05
46.Fisher-exact testMA0030.1FOXF2top 1126 seqs3.078e-081.638e-05
47.Fisher-exact testUP00075_1Sox15_primarytop 1126 seqs3.231e-081.719e-05
48.Fisher-exact testUP00046_1Tcfe2a_primarytop 1126 seqs3.242e-081.725e-05
49.Fisher-exact testUP00025_1Foxk1_primarytop 1126 seqs3.489e-081.856e-05
50.Fisher-exact testUP00079_1Esrra_primarytop 1126 seqs3.532e-081.879e-05
51.Fisher-exact testUP00016_2Sry_secondarytop 1126 seqs3.729e-081.984e-05
52.Fisher-exact testUP00041_1Foxj1_primarytop 1126 seqs4.365e-082.322e-05
53.Fisher-exact testUP00408_1Gabpa_primarytop 1126 seqs4.366e-082.323e-05
54.Fisher-exact testMA0062.2GABPAtop 1126 seqs4.99e-082.655e-05
55.Fisher-exact testMA0039.1Klf4top 1126 seqs6.63e-083.527e-05
56.Fisher-exact testUP00064_1Sox18_primarytop 1126 seqs7.436e-083.956e-05
57.Fisher-exact testMA0004.1Arnttop 1126 seqs7.562e-084.023e-05
58.Fisher-exact testMA0093.1USF1top 1126 seqs7.562e-084.023e-05
59.Fisher-exact testMA0104.1Mycntop 1126 seqs7.562e-084.023e-05
60.Fisher-exact testUP00255_1Dbx1_3486.1top 1126 seqs1.088e-075.786e-05
61.Fisher-exact testMA0144.1Stat3top 1126 seqs1.362e-077.243e-05
62.Fisher-exact testUP00022_1Zfp740_primarytop 1126 seqs1.43e-077.607e-05
63.Fisher-exact testUP00039_1Foxj3_primarytop 1126 seqs1.915e-070.0001019
64.Fisher-exact testMA0141.1Esrrbtop 1126 seqs2.092e-070.0001113
65.Fisher-exact testMA0137.2STAT1top 1126 seqs2.626e-070.0001397
66.Fisher-exact testMA0069.1Pax6top 1126 seqs3.363e-070.0001789