$1 = the input file name

$3 = the maximum percentage similarity between motif content of modules.

According to the similarity, closed modules that show this minimum percentage of similarity with other modules, will be deleted from the list. This parameter can thus be considered a filter. We choose however to set this parameter to 100 by default, such that no modules are filtered. ModuleDigger will do the filtering of the modules based on a statistical framework (see section 2.3).

$4 = support threshold.

This is the percent of genes that should have the CRM. If there are for instance 100 genes, and at least 2 genes should have this CRM, this parameter should be set to 2/100=0.02.

$5 = minimum number of motifs in the module

$6 = maximum number of motifs in the module

An example of the output from ModuleDigger is given below. The application of chromatin immunoprecipitation combined with DNA microarray techniques (ChIP-Chip) in eukaryotes allows the genome wide mapping of the physical interaction between a TF and its target gene. The test set we composed was derived from a genomewide ChIP-Chip analysis performed by Boyer et al. 2005 [1]. It consists of 116 genes that co-bind three core TFs, OCT4, SOX2, NANOG (involved in plurypotency and self-renewal) in their 1000 bp proximal promoter region. Moreover, the three TFs bind in each other close proximity turning them in a true case example of a CRM.

[hsun@grimbergen ~]$ sh prepareData.sh 116 1 100 0.03 2 3


-73.29355547318917 # motif2 motif7 motif1 % 2 4 6 7 8 10 16 35 38 46 47 50 51 52 56 60 63 64 65 66 70 71 77 78 79 84 86 89 94 95 96 101 102 103 105 107 108 109 110 111 112 113 114 117
-49.24703169089435 # motif8 motif7 motif1 % 6 7 8 9 10 16 24 33 34 36 38 42 43 47 50 52 61 62 64 65 66 67 77 78 84 86 90 94 95 96 105
-42.69958057831979 # motif8 motif10 motif1 % 6 7 10 11 16 17 18 19 20 23 27 28 29 33 34 36 37 38 42 43 61 62 67 74 75 76 78 86 90 94 95 105
-42.20133956971947 # motif10 motif7 motif1 % 2 4 6 7 10 16 33 34 35 36 38 40 41 42 43 46 51 61 62 67 70 71 78 86 90 94 95 105 108 117
-34.235962332291 # motif8 motif2 motif1 % 6 7 8 10 16 20 38 47 49 50 52 64 65 66 74 75 76 77 78 80 83 84 86 94 95 96 105
-32.65380109797474 # motif3 motif2 motif1 % 1 4 16 20 30 35 38 46 47 51 56 60 63 64 65 66 74 75 76 78 83 84 89 94 95 96 105 107 112 113 114 117
-30.043878166763363 # motif5 motif2 motif7 % 10 16 38 45 46 47 50 51 52 70 71 77 79 84 86 89 94 95 101 102 103 105 106 107 112 113 114 117
-29.983890535762075 # motif3 motif2 motif7 % 4 16 35 38 45 46 47 51 56 60 63 64 65 66 78 84 89 94 95 96 105 107 112 113 114 117
-28.902694100897392 # motif3 motif7 motif1 % 4 16 33 35 38 40 41 44 46 47 51 56 60 63 64 65 66 78 84 89 90 94 95 96 105 107 112 113 114 117
-27.904620008389834 # motif5 motif7 motif1 % 10 16 36 38 40 41 46 47 48 50 51 52 61 70 71 77 79 84 86 89 94 95 101 102 103 105 107 112 113 114 117
-27.868372818297626 # motif8 motif7 motif10 % 3 6 7 10 16 33 34 36 38 42 43 61 62 67 78 86 90 94 95 105 106 115 116
-27.473634009382067 # motif5 motif2 motif1 % 10 16 20 31 38 46 47 49 50 51 52 70 71 77 79 84 86 89 94 95 101 102 103 105 107 112 113 114 117
-26.267720386059583 # motif10 motif2 motif7 % 2 3 4 6 7 10 16 35 38 45 46 51 58 59 70 71 78 86 94 95 104 105 106 108 117
-23.456762388126865 # motif4 motif3 motif1 % 1 4 12 13 20 27 28 29 40 41 53 54 55 78 83 107 112 113 114
-21.606420390540983 # motif8 motif2 motif7 % 3 6 7 8 10 16 38 47 50 52 64 65 66 77 78 84 86 94 95 96 105 106
-21.377855448602926 # motif3 motif10 motif1 % 4 11 16 20 27 28 29 33 35 37 38 40 41 46 51 74 75 76 78 82 87 90 94 95 105 117
-20.867294295882605 # motif10 motif2 motif1 % 2 4 6 7 10 16 20 35 38 46 51 70 71 74 75 76 78 86 94 95 105 108 117
-20.553940923874787 # motif4 motif2 motif7 % 3 4 8 45 50 58 59 78 107 109 110 111 112 113 114
-19.352853257799747 # motif6 motif3 motif1 % 1 4 11 16 30 35 40 41 47 51 74 75 76 82 83 87 90 94 95 96 105 117
-19.101478172007607 # motif4 motif2 motif1 % 1 4 8 20 31 50 78 80 83 107 109 110 111 112 113 114
-19.051073424035213 # motif6 motif2 motif10 % 2 3 4 10 16 25 26 35 51 74 75 76 94 95 97 105 106 117
-18.488604495802292 # motif5 motif10 motif7 % 10 16 36 38 40 41 45 46 51 61 70 71 86 94 95 105 106 115 116 117
-18.318020060719437 # motif6 motif7 motif1 % 2 4 9 10 16 24 35 36 40 41 47 48 51 79 90 94 95 96 105 117
-17.92027219046008 # motif3 motif8 motif10 % 11 16 20 27 28 29 33 37 38 68 69 74 75 76 78 90 94 95 105 115 116
-17.915867039377076 # motif3 motif8 motif1 % 11 16 20 27 28 29 33 37 38 47 64 65 66 74 75 76 78 83 84 90 94 95 96 105
-17.765768029029026 # motif4 motif5 motif1 % 12 17 18 19 20 27 28 29 31 40 41 50 107 112 113 114
-17.036852962309666 # motif6 motif5 motif2 % 10 16 25 26 31 47 51 79 91 92 94 95 105 106 117
-16.981263808308913 # motif6 motif3 motif10 % 4 11 16 35 40 41 51 57 74 75 76 82 87 90 94 95 105 117
-16.96119614747447 # motif5 motif8 motif10 % 10 16 17 18 19 20 23 25 26 27 28 29 36 38 61 86 94 95 105 106 115 116
-16.571575811949128 # motif6 motif2 motif1 % 1 2 4 10 16 30 31 35 47 51 74 75 76 79 80 83 94 95 96 105 117


$1            =            116.txt
$2            =            1
$3            =            100
$4            =            0.03
$5            =            2
$6            =            3

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