Experiments with random sets of genes (mouse genes, raw sequences)
Nomenclature and parameters
Summary of results
Summary of results
  max_n_motifs=2       max_n_motifs=3       max_n_motifs=4           seq. length seq. length n_s
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
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
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          
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          
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          
25 0 nan nan nan nan 0 nan nan nan nan 0 nan nan nan nan random2 458 7453 2786 20
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          
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          
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          
25 0 nan nan nan nan 0 nan nan nan nan 0 nan nan nan nan random3 358 8268 2223 20
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          
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          
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          
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
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          
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          
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          
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
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          
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          
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          
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
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    
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    
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          
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
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    
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    
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          
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
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    
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    
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          
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
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    
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    
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          
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
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    
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    
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          
25 0 nan nan nan nan 0 nan nan nan nan 0 nan nan nan nan random11 302 8515 1946 40
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          
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          
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          
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
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          
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          
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          
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
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          
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
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)
Other parameters:
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