| Experiments with random sets of genes (mouse genes, raw
sequences) |
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| Nomenclature and
parameters |
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| Summary of results |
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| Summary of results |
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max_n_motifs=2 |
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max_n_motifs=3 |
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max_n_motifs=4 |
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seq. length |
seq. length |
n_s |
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| max_d |
n_check |
median1 |
min1 |
median2 |
min2 |
n_check |
median1 |
min1 |
median2 |
min2 |
n_check |
median1 |
min1 |
median2 |
min2 |
id |
n_motifs |
mean |
s.d. |
number of genes in set |
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| 25 |
2 |
1.2E-05 |
7.0E-06 |
1.8E-01 |
1.8E-01 |
3 |
1.6E-05 |
7.0E-06 |
1.8E-01 |
1.8E-01 |
7 |
2.2E-06 |
1.1E-07 |
1.0E+00 |
1.8E-01 |
random 1 |
480 |
7613 |
2671 |
20 |
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| 50 |
1 |
3.0E-06 |
3.0E-06 |
1.0E+00 |
1.0E+00 |
13 |
1.5E-05 |
1.7E-06 |
1.0E+00 |
2.1E-03 |
48 |
4.0E-06 |
1.6E-07 |
1.8E-01 |
1.4E-04 |
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| 100 |
4 |
1.5E-05 |
6.9E-06 |
1.8E-01 |
5.3E-03 |
15 |
3.7E-06 |
6.9E-08 |
1.0E+00 |
1.8E-03 |
52 |
5.0E-05 |
1.6E-07 |
1.1E-01 |
3.0E-05 |
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| 200 |
10 |
1.7E-04 |
6.5E-06 |
5.9E-01 |
2.4E-03 |
23 |
1.8E-06 |
4.8E-07 |
1.0E+00 |
5.7E-04 |
42 |
3.5E-05 |
5.7E-08 |
3.4E-03 |
4.8E-05 |
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| 25 |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
random2 |
458 |
7453 |
2786 |
20 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
4 |
1.1E-05 |
2.9E-06 |
1.0E+00 |
1.0E+00 |
5 |
1.2E-05 |
1.4E-08 |
1.0E+00 |
1.5E-02 |
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| 100 |
0 |
nan |
nan |
nan |
nan |
5 |
9.7E-06 |
3.2E-07 |
1.2E-01 |
8.4E-02 |
35 |
1.3E-05 |
3.2E-06 |
1.0E+00 |
3.0E-04 |
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| 200 |
0 |
nan |
nan |
nan |
nan |
6 |
5.8E-06 |
2.3E-07 |
5.9E-01 |
1.3E-01 |
57 |
3.3E-06 |
1.3E-08 |
1.0E+00 |
3.4E-04 |
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| 25 |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
random3 |
358 |
8268 |
2223 |
20 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
10 |
8.3E-05 |
2.6E-07 |
1.0E+00 |
1.8E-01 |
37 |
6.7E-05 |
2.6E-06 |
1.0E+00 |
2.6E-04 |
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| 100 |
0 |
nan |
nan |
nan |
nan |
4 |
6.5E-05 |
3.5E-05 |
5.9E-01 |
1.8E-01 |
45 |
6.8E-05 |
5.3E-07 |
1.0E+00 |
3.4E-04 |
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| 200 |
0 |
nan |
nan |
nan |
nan |
1 |
1.0E-06 |
1.0E-06 |
1.8E-01 |
1.8E-01 |
32 |
8.1E-05 |
3.0E-06 |
1.0E+00 |
2.1E-04 |
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| 25 |
1 |
3.7E-06 |
3.7E-06 |
5.6E-02 |
5.6E-02 |
3 |
2.8E-05 |
3.7E-07 |
1.0E+00 |
1.5E-02 |
3 |
2.8E-05 |
3.7E-07 |
1.0E+00 |
1.5E-02 |
random4 |
538 |
8078 |
2277 |
20 |
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| 50 |
2 |
5.0E-05 |
2.5E-06 |
5.9E-01 |
1.8E-01 |
9 |
2.6E-06 |
1.2E-07 |
1.0E+00 |
1.8E-01 |
10 |
9.0E-06 |
1.2E-07 |
1.0E+00 |
7.2E-02 |
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| 100 |
4 |
2.6E-06 |
2.0E-06 |
1.0E+00 |
1.8E-01 |
18 |
1.6E-05 |
8.1E-08 |
1.0E+00 |
1.8E-01 |
39 |
3.3E-06 |
1.2E-07 |
1.0E+00 |
7.5E-05 |
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| 200 |
3 |
1.6E-05 |
6.2E-06 |
1.0E+00 |
1.4E-02 |
16 |
9.2E-06 |
9.7E-08 |
1.0E+00 |
2.3E-03 |
43 |
2.7E-06 |
9.6E-08 |
1.0E+00 |
2.5E-05 |
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| 25 |
2 |
9.3E-07 |
9.3E-07 |
1.0E+00 |
1.0E+00 |
2 |
9.3E-06 |
9.3E-07 |
1.0E+00 |
1.0E+00 |
2 |
9.3E-05 |
9.3E-05 |
1.0E+00 |
1.0E+00 |
random5 |
518 |
7981 |
2085 |
20 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
6 |
6.2E-06 |
2.1E-06 |
7.5E-02 |
4.7E-03 |
7 |
7.6E-05 |
9.5E-07 |
1.0E+00 |
2.1E-03 |
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| 100 |
0 |
nan |
nan |
nan |
nan |
4 |
2.3E-05 |
1.6E-07 |
1.0E+00 |
1.0E+00 |
35 |
5.1E-06 |
6.0E-07 |
1.0E+00 |
1.5E-04 |
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| 200 |
2 |
1.1E-06 |
5.9E-07 |
1.8E-01 |
1.8E-01 |
13 |
1.3E-05 |
4.8E-07 |
1.8E-01 |
1.8E-01 |
40 |
2.9E-05 |
3.8E-07 |
1.0E+00 |
3.0E-04 |
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| 25 |
1 |
3.2E-04 |
3.2E-04 |
1.4E-02 |
1.4E-02 |
1 |
3.2E-04 |
3.2E-04 |
1.4E-02 |
1.4E-02 |
2 |
2.6E-04 |
2.0E-04 |
5.0E-01 |
7.7E-03 |
random 6 |
398 |
8458 |
2172 |
30 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
1 |
3.0E-06 |
3.0E-06 |
2.5E-01 |
2.5E-01 |
6 |
1.2E-05 |
1.4E-07 |
1.0E+00 |
2.5E-01 |
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| 100 |
0 |
nan |
nan |
nan |
nan |
4 |
3.0E-05 |
8.7E-06 |
1.0E+00 |
6.4E-03 |
22 |
1.2E-05 |
1.5E-07 |
1.0E+00 |
1.8E-03 |
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| 200 |
0 |
nan |
nan |
nan |
nan |
2 |
8.0E-05 |
4.5E-05 |
5.8E-01 |
1.6E-01 |
22 |
1.9E-05 |
2.3E-07 |
1.0E+00 |
1.4E-03 |
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| 25 |
1 |
5.8E-07 |
5.8E-07 |
8.3E-03 |
8.3E-03 |
2 |
1.6E-05 |
5.8E-08 |
5.0E-01 |
8.3E-03 |
9 |
4.2E-06 |
5.8E-08 |
1.0E+00 |
2.4E-03 |
random7 |
497 |
8626 |
2233 |
30 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
3 |
2.3E-05 |
4.5E-06 |
3.3E-02 |
3.3E-02 |
22 |
9.2E-06 |
3.3E-08 |
1.0E+00 |
1.8E-04 |
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| 100 |
1 |
2.8E-05 |
2.8E-05 |
1.9E-02 |
1.9E-02 |
7 |
1.2E-05 |
8.9E-07 |
1.0E+00 |
2.0E-03 |
56 |
4.8E-05 |
2.4E-06 |
1.0E+00 |
2.5E-05 |
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| 200 |
5 |
1.1E-05 |
1.5E-06 |
3.6E-03 |
2.9E-03 |
32 |
9.4E-07 |
7.5E-08 |
6.8E-04 |
4.9E-04 |
62 |
4.7E-06 |
3.3E-07 |
1.1E-02 |
7.8E-05 |
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| 25 |
0 |
nan |
nan |
nan |
nan |
3 |
1.0E-05 |
9.6E-06 |
2.5E-01 |
2.5E-01 |
3 |
1.0E-05 |
9.6E-06 |
2.5E-01 |
2.5E-01 |
random8 |
407 |
8249 |
2218 |
30 |
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| 50 |
7 |
1.4E-05 |
6.6E-07 |
1.0E+00 |
1.0E+00 |
11 |
2.9E-06 |
6.6E-07 |
1.0E+00 |
2.1E-01 |
25 |
1.7E-05 |
8.4E-08 |
1.0E+00 |
2.1E-01 |
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| 100 |
16 |
3.3E-04 |
2.5E-07 |
1.0E+00 |
3.3E-02 |
34 |
7.7E-06 |
2.5E-07 |
1.0E+00 |
3.3E-02 |
63 |
2.8E-06 |
5.3E-08 |
1.0E+00 |
3.3E-02 |
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| 200 |
28 |
6.0E-05 |
3.4E-07 |
1.0E+00 |
2.9E-03 |
37 |
2.4E-06 |
6.0E-08 |
1.0E+00 |
2.9E-03 |
62 |
4.3E-06 |
3.0E-09 |
1.0E+00 |
2.9E-03 |
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| 25 |
1 |
1.5E-04 |
1.5E-04 |
1.0E+00 |
1.0E+00 |
2 |
8.1E-05 |
1.6E-05 |
5.7E-01 |
1.3E-01 |
2 |
8.1E-05 |
1.6E-05 |
5.7E-01 |
1.3E-01 |
random9 |
393 |
7309 |
2377 |
30 |
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| 50 |
0 |
nan |
nan |
nan |
nan |
1 |
9.0E-06 |
9.0E-06 |
1.0E+00 |
1.0E+00 |
9 |
9.0E-06 |
2.7E-08 |
1.0E+00 |
2.5E-01 |
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| 100 |
2 |
2.2E-06 |
4.6E-07 |
6.3E-01 |
2.5E-01 |
2 |
2.2E-06 |
4.6E-07 |
6.3E-01 |
2.5E-01 |
18 |
1.7E-05 |
1.2E-07 |
1.0E+00 |
3.3E-02 |
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| 200 |
5 |
7.4E-06 |
9.6E-07 |
2.5E-01 |
2.5E-01 |
8 |
1.3E-05 |
9.6E-08 |
1.0E+00 |
2.5E-01 |
41 |
8.6E-05 |
1.3E-07 |
1.0E+00 |
1.0E-01 |
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| 25 |
0 |
nan |
nan |
nan |
nan |
4 |
1.1E-05 |
6.5E-06 |
1.0E+00 |
1.8E-01 |
4 |
1.1E-05 |
6.5E-06 |
1.0E+00 |
1.8E-01 |
random10 |
334 |
7861 |
2212 |
30 |
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| 50 |
3 |
1.5E-06 |
1.7E-07 |
3.3E-02 |
3.3E-02 |
4 |
8.1E-06 |
1.4E-07 |
5.2E-01 |
3.3E-02 |
8 |
1.2E-05 |
1.4E-07 |
1.0E+00 |
3.3E-02 |
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| 100 |
7 |
5.2E-07 |
3.3E-08 |
3.3E-02 |
2.4E-03 |
19 |
2.1E-06 |
1.3E-08 |
2.5E-01 |
1.5E-03 |
55 |
6.9E-06 |
1.3E-08 |
1.0E+00 |
6.0E-04 |
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|
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|
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| 200 |
12 |
1.1E-06 |
7.1E-08 |
3.3E-02 |
1.5E-03 |
39 |
2.8E-05 |
9.1E-07 |
3.3E-02 |
1.8E-04 |
64 |
1.5E-06 |
7.7E-08 |
1.0E+00 |
8.5E-04 |
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| 25 |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
0 |
nan |
nan |
nan |
nan |
random11 |
302 |
8515 |
1946 |
40 |
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| 50 |
1 |
5.6E-06 |
5.6E-06 |
1.0E+00 |
1.0E+00 |
3 |
5.6E-06 |
8.7E-07 |
1.0E+00 |
3.2E-01 |
7 |
7.2E-05 |
1.1E-07 |
1.0E+00 |
8.5E-02 |
|
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|
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|
|
| 100 |
5 |
1.1E-05 |
2.8E-08 |
5.6E-02 |
2.0E-03 |
10 |
7.1E-06 |
2.8E-08 |
6.6E-01 |
1.3E-03 |
23 |
5.8E-06 |
1.1E-08 |
1.0E+00 |
1.1E-03 |
|
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|
|
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|
|
| 200 |
3 |
3.3E-04 |
1.5E-08 |
3.2E-01 |
5.4E-02 |
17 |
1.9E-06 |
4.1E-08 |
1.0E+00 |
5.4E-02 |
67 |
1.1E-06 |
3.5E-08 |
1.0E+00 |
1.0E-02 |
|
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|
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| 25 |
0 |
nan |
1.0E+07 |
nan |
nan |
1 |
2.8E-05 |
2.8E-05 |
1.4E-01 |
1.4E-01 |
1 |
2.8E-05 |
2.8E-05 |
1.4E-01 |
1.4E-01 |
random12 |
387 |
8158 |
1942 |
40 |
|
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|
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| 50 |
0 |
nan |
1.0E+07 |
nan |
nan |
2 |
1.1E-03 |
1.7E-05 |
1.0E+00 |
1.0E+00 |
14 |
9.2E-06 |
4.4E-07 |
1.0E+00 |
1.1E-01 |
|
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|
|
|
|
|
| 100 |
2 |
3.0E-05 |
8.7E-06 |
6.6E-01 |
3.2E-01 |
4 |
1.6E-05 |
1.7E-06 |
6.6E-01 |
1.1E-01 |
22 |
1.2E-05 |
2.0E-08 |
1.0E+00 |
2.1E-02 |
|
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|
|
|
|
|
|
| 200 |
3 |
3.6E-06 |
5.2E-07 |
4.4E-03 |
3.9E-03 |
4 |
7.0E-06 |
5.2E-07 |
5.0E-01 |
3.9E-03 |
36 |
7.2E-04 |
5.4E-08 |
1.0E+00 |
1.0E-03 |
|
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| 25 |
1 |
4.2E-05 |
4.2E-05 |
3.2E-01 |
3.2E-01 |
1 |
4.2E-05 |
4.2E-05 |
3.2E-01 |
3.2E-01 |
1 |
4.2E-05 |
4.2E-05 |
3.2E-01 |
3.2E-01 |
random13 |
352 |
7699 |
2100 |
40 |
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| 50 |
3 |
3.4E-06 |
1.3E-06 |
7.1E-03 |
6.5E-03 |
4 |
3.9E-06 |
1.3E-06 |
1.6E-01 |
6.5E-03 |
4 |
4.6E-06 |
1.3E-06 |
1.0E+00 |
2.6E-03 |
|
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|
|
|
|
|
|
|
| 100 |
2 |
7.5E-07 |
6.1E-07 |
5.0E-01 |
6.5E-03 |
2 |
7.5E-06 |
6.1E-07 |
5.0E-01 |
6.5E-03 |
9 |
1.1E-05 |
5.4E-07 |
1.0E+00 |
6.5E-03 |
|
|
|
|
|
|
|
|
|
| 200 |
9 |
1.3E-05 |
3.2E-07 |
3.9E-03 |
5.5E-04 |
21 |
9.5E-06 |
1.9E-08 |
6.5E-03 |
5.5E-04 |
24 |
1.4E-06 |
1.4E-07 |
3.2E-01 |
3.6E-04 |
|
|
|
|
|
|
|
|
|
| 25 |
1 |
2.9E-05 |
2.9E-05 |
1.0E+00 |
1.0E+00 |
2 |
3.2E-05 |
2.9E-05 |
1.0E+00 |
1.0E+00 |
2 |
3.2E-05 |
2.9E-05 |
1.0E+00 |
1.0E+00 |
random14 |
395 |
7713 |
1768 |
40 |
|
|
|
|
| 50 |
1 |
2.9E-04 |
2.9E-04 |
1.0E+00 |
1.0E+00 |
3 |
8.5E-06 |
3.5E-07 |
1.0E+00 |
1.0E+00 |
23 |
7.1E-03 |
3.5E-07 |
1.0E+00 |
3.6E-02 |
|
|
|
|
|
|
|
|
|
| 100 |
0 |
nan |
nan |
nan |
nan |
1 |
2.9E-05 |
2.9E-05 |
1.0E+00 |
1.0E+00 |
26 |
4.7E-03 |
2.0E-08 |
1.0E+00 |
1.5E-04 |
|
|
|
|
|
|
|
|
|
| 200 |
0 |
nan |
nan |
nan |
nan |
1 |
8.7E-08 |
8.7E-08 |
1.0E+00 |
1.0E+00 |
25 |
2.1E-03 |
2.8E-08 |
1.0E+00 |
4.0E-02 |
|
|
|
|
|
|
|
|
|
| 25 |
1 |
2.0E-07 |
2.0E-07 |
3.2E-01 |
3.2E-01 |
1 |
2.0E-07 |
2.0E-07 |
3.2E-01 |
3.2E-01 |
1 |
2.0E-07 |
2.0E-07 |
3.2E-01 |
3.2E-01 |
random15 |
384 |
7427 |
2215 |
40 |
|
|
|
|
| 50 |
1 |
7.6E-07 |
7.6E-07 |
3.2E-01 |
3.2E-01 |
2 |
1.3E-05 |
7.6E-07 |
6.6E-01 |
3.2E-01 |
8 |
1.4E-06 |
7.1E-08 |
1.0E+00 |
2.0E-02 |
|
|
|
|
|
|
|
|
|
| 100 |
3 |
2.8E-06 |
1.7E-06 |
7.0E-03 |
6.5E-03 |
5 |
2.8E-06 |
4.1E-07 |
1.0E+00 |
6.5E-03 |
10 |
5.8E-06 |
3.5E-07 |
1.0E+00 |
5.5E-04 |
|
|
|
|
|
|
|
|
|
| 200 |
13 |
2.3E-07 |
4.4E-08 |
6.5E-03 |
5.5E-04 |
21 |
2.1E-06 |
3.5E-08 |
5.6E-02 |
5.5E-04 |
24 |
8.5E-07 |
3.8E-08 |
1.0E+00 |
3.6E-05 |
|
|
|
|
|
|
|
|
|
| mean |
2.8 |
5.2E-05 |
5.0E+05 |
4.3E-01 |
2.6E-01 |
7.9 |
4.0E-05 |
1.1E-05 |
6.4E-01 |
2.4E-01 |
23.7 |
2.8E-04 |
7.8E-06 |
8.5E-01 |
8.6E-02 |
|
413.4 |
7960.4 |
|
mean |
|
|
|
|
| std |
4.8 |
9.9E-05 |
2.2E+06 |
4.1E-01 |
3.7E-01 |
9.5 |
1.5E-04 |
4.3E-05 |
3.8E-01 |
3.5E-01 |
20.6 |
1.1E-03 |
3.0E-05 |
3.1E-01 |
2.0E-01 |
|
69.7 |
418.9 |
|
std |
|
|
|
|
| min |
0.0 |
2.0E-07 |
1.5E-08 |
3.6E-03 |
5.5E-04 |
0.0 |
8.7E-08 |
1.3E-08 |
6.8E-04 |
1.8E-04 |
0.0 |
2.0E-07 |
3.0E-09 |
3.4E-03 |
2.5E-05 |
|
302.0 |
7308.8 |
|
min |
|
|
|
|
| max |
28.0 |
3.3E-04 |
1.0E+07 |
1.0E+00 |
1.0E+00 |
39.0 |
1.1E-03 |
3.2E-04 |
1.0E+00 |
1.0E+00 |
67.0 |
7.1E-03 |
2.0E-04 |
1.0E+00 |
1.0E+00 |
|
538.0 |
8626.3 |
|
max |
|
|
|
|
| median |
1.0 |
9.2E-06 |
1.4E-06 |
3.2E-01 |
4.4E-02 |
4.0 |
9.5E-06 |
6.1E-07 |
6.6E-01 |
1.3E-01 |
22.2 |
1.2E-05 |
1.4E-07 |
1.0E+00 |
2.9E-03 |
|
395.0 |
7981.3 |
|
median |
|
|
|
|
| |
max_n_motifs=2 |
mm |
|
hs |
max_n_motifs=3 |
mm |
|
hs |
max_n_motifs=4 |
mm |
|
hs |
|
|
|
|
|
|
|
|
|
| |
n_check |
median1 |
min1 |
median2 |
min2 |
n_check |
median1 |
min1 |
median2 |
min2 |
n_check |
median1 |
min1 |
median2 |
min2 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Nomenclature and parameters |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| n_s |
number of random mouse genes used as input to
the program (20, 30 or 40) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| n_motifs |
total number of motifs |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| max_n_motifs |
maximum number of motifs in a module (2, 3 or 4) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| max_d |
maximum distance between motifs (25, 50, 100 or
200 bp) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| n_module |
number of module predictions |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| median1 |
median enrichment p value for mouse |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| min1 |
best (minimum) p value for all the modules for mouse |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| median2 |
median enrichment p value for the same modules in humans |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| min2 |
best (minimum) p value for the same modules in humans |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| Note: If the
output was 0 modules (n_module=0), then the p values are nan (not a number) |
|
|
|
|
|
|
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|
|
| Other
parameters: |
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
| maximum
upstream length = 5000 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| maximum exon
length = 5000 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| maximum intron
length = 5000 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| motif
comparison threshold = 70 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| reverse strand
= true |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| scan threshold
= min_fn |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| minimum genes
with module = 4 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| order = false |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| sequence source
= ncbi |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| mask
non-conserved = false |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|