{"text_format":"3","workbook":"xls","n_sheets":3,"sheets":["Ark1","Ark2","Ark3"],"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"Ark1","index":0,"n_rows":154,"n_cols":16,"rows_kept":154,"flags":["formulas_cached_only"]}
["Statistics of datasets used for the composite motif discovery assessment"]
[]
[]
["TRANSCompel dataset "]
[]
["Sequence set","Sequences","Min seq. length","Max seq. length","Avg. seq. length","Total seq length","Modules","min module size (bp)","max module size (bp)","avg. module size (bp)","Std. module size (bp)","Lowest PWM IC-content","Sum of PWMs IC-content","Module/background"]
["AP1-Ets",16,609,1000,{"v":928.75,"d":"929"},14860,17,14,99,{"v":26.52941176,"d":"26.53"},21.43,{"v":8.75714755,"d":"8.76"},{"v":17.77801145,"d":"17.78"},{"v":0.029407806,"d":"0.02941"}]
["AP1-NFAT",8,294,1000,{"v":861.625,"d":"862"},6893,11,14,19,{"v":16.36363636,"d":"16.36"},{"v":1.3667,"d":"1.37"},{"v":8.75714755,"d":"8.76"},{"v":18.381045972,"d":"18.38"},{"v":0.026113448,"d":"0.02611"}]
["AP1-NFkB",7,532,1000,{"v":933.1428571,"d":"933"},6532,8,18,135,{"v":53.125,"d":"53.13"},{"v":34.919,"d":"34.92"},{"v":8.75714755,"d":"8.76"},{"v":19.48623661,"d":"19.49"},{"v":0.059399878,"d":"0.05940"}]
["CEBP-NFkB",8,308,1000,{"v":913.5,"d":"914"},7308,8,44,118,{"v":83.5,"d":"83.50"},{"v":25.129,"d":"25.13"},{"v":9.737109566,"d":"9.74"},{"v":20.466198626,"d":"20.47"},{"v":0.091406678,"d":"0.09141"}]
["Ebox-Ets",4,492,1000,{"v":872.25,"d":"872"},3489,6,16,50,{"v":25.16666667,"d":"25.17"},{"v":11.378,"d":"11.38"},{"v":9.0208639,"d":"9.02"},{"v":20.835106500000002,"d":"20.84"},{"v":0.03955288,"d":"0.03955"}]
["Ets-AML",5,480,1000,{"v":810.6,"d":"811"},4053,5,13,30,{"v":19,"d":"19.00"},{"v":6.418,"d":"6.42"},{"v":9.0208639,"d":"9.02"},{"v":20.6767279,"d":"20.68"},{"v":0.023439427999999998,"d":"0.02344"}]
["IRF-NFkB",6,596,1000,{"v":890.6666667,"d":"891"},5344,6,23,71,{"v":42.83333333,"d":"42.83"},{"v":16.856,"d":"16.86"},{"v":10.72908906,"d":"10.73"},{"v":24.79644166,"d":"24.80"},{"v":0.048091317,"d":"0.04809"}]
["NFkB-HMGIY",6,393,1000,{"v":898.8333333,"d":"899"},5393,7,10,32,{"v":13.28571429,"d":"13.29"},{"v":7.647,"d":"7.65"},{"v":9.132071507061,"d":"9.13"},{"v":19.861160567061,"d":"19.86"},{"v":0.017244576,"d":"0.01724"}]
["PU1-IRF",5,722,1000,906,4530,5,12,14,{"v":13,"d":"13.00"},{"v":0.8944,"d":"0.89"},{"v":13.0761468,"d":"13.08"},{"v":27.1434994,"d":"27.14"},{"v":0.014348786,"d":"0.01435"}]
["Sp1-Ets",7,309,1000,{"v":826.7142857,"d":"827"},5787,8,16,117,{"v":36.5,"d":"36.50"},{"v":31.823,"d":"31.82"},{"v":9.0208639,"d":"9.02"},{"v":19.44506038,"d":"19.45"},{"v":0.04838431,"d":"0.04838"}]
["Average",7.2,{"v":473.5,"d":"474"},1000,{"v":884.20821428,"d":"884"},{"v":6418.9,"d":"6419"},8.1,18,68.5,{"v":32.930376241,"d":"32.93"},{"v":15.786110000000003,"d":"15.79"},{"v":9.6008451283061,"d":"9.60"},{"v":20.8869489065061,"d":"20.89"},{"v":0.039738910700000005,"d":"0.03974"}]
["Sum",72,{"$nulls":4},81]
[null,"Numer of sequences","size of smallest",null,null,"total number of bases in","Number of module","size of the smallest module",null,null,"standard deviation of module","The information content of","The sum of information ","The ratio of module"]
[null,"in each sequence set","sequence in set",null,null,"each sequence set","occurrences (of the","in each sequence set",null,null,"sizes","the custom PWM with the  ","content for the two custom","nucleotides to"]
[{"$nulls":5},"(summed over all","correct class) in each",{"$nulls":4},"lowest information content","PWMs used for each ","background nucleotides"]
[{"$nulls":5},"sequences)","sequence set",{"$nulls":4},"of the two used for each","sequence set","across the whole"]
["11 TRANSCompel sequences contain more than one module: 7 sequences contain 2 modules, 4 contain 3 modules and 1 contains 4 modules",{"$nulls":10},"sequence set",null,"sequence set"]
["Maximum number of modules of the same class within a single sequence = 3     (module:Ebox-Ets, sequence: V01523). "]
["Maximum number of different classes of modules in a sequence = 3     (sequence: V00534, modules: AP1-NFkB, IRF-NFkB, NFkB-HMGIY)"]
["(Only modules of the specified classes were considered)"]
[]
[]
["TRANSCompel custom PWMs"]
[]
["Motif","module classes","binding patterns","size (bp)","Information content (IC)"]
["AML",1,7,8,{"v":11.655864,"d":"11.66"}]
["AP1",3,42,8,{"v":8.75714755,"d":"8.76"}]
["CEBP",1,15,8,{"v":9.737109566,"d":"9.74"}]
["Ebox",1,5,8,{"v":11.8142426,"d":"11.81"}]
["Ets",4,47,8,{"v":9.0208639,"d":"9.02"}]
["HMGIY",1,13,8,{"v":9.132071507061,"d":"9.13"}]
["IRF",2,14,8,{"v":14.0673526,"d":"14.07"}]
["NFAT",1,15,8,{"v":9.623898422,"d":"9.62"}]
["NFkB",3,38,10,{"v":10.72908906,"d":"10.73"}]
["PU1",1,7,8,{"v":13.0761468,"d":"13.08"}]
["Sp1",1,9,8,{"v":10.42419648,"d":"10.42"}]
["Average",{"v":1.7272727272727273,"d":"1.7"},{"v":19.272727272727273,"d":"19.3"},{"v":8.181818181818182,"d":"8.2"},{"v":10.730725680460091,"d":"10.7"}]
["Median",{"v":1,"d":"1.0"},{"v":14,"d":"14.0"},{"v":8,"d":"8.0"},{"v":10.42419648,"d":"10.4"}]
[]
[null,"Number of module","Number of binding site"]
[null,"classes that the TFs","patterns used to "]
[null,"were a part of","construct each PWM"]
[]
[]
[]
["TRANSCompel Transfac PWMs"]
[]
["Motif","PWMs in set","minimum size (bp)","maximum size (bp)","average size (bp)","minimum IC","Maximum IC","average IC"]
["AML",4,6,15,{"v":11,"d":"11.0"},{"v":11.4967416652244,"d":"11.4967"},{"v":13.1076370264472,"d":"13.1076"},{"v":12.2875098824988,"d":"12.2875"}]
["AP1",19,6,18,{"v":11.1578947368421,"d":"11.2"},{"v":7.95105668441713,"d":"7.9511"},{"v":23.1829175195343,"d":"23.1829"},{"v":12.4598513968867,"d":"12.4599"}]
["CEBP",9,12,14,{"v":13.1111111111111,"d":"13.1"},{"v":6.41569184346492,"d":"6.4157"},{"v":12.3672766230995,"d":"12.3673"},{"v":8.86591593716922,"d":"8.8659"}]
["Ebox",12,6,18,{"v":11.75,"d":"11.8"},{"v":8.97798660748707,"d":"8.9780"},{"v":21.4563459160504,"d":"21.4563"},{"v":11.6724492225626,"d":"11.6724"}]
["Ets",14,7,16,{"v":11.7857142857143,"d":"11.8"},{"v":8.81537798817042,"d":"8.8154"},{"v":16.9436093777043,"d":"16.9436"},{"v":12.1980134051171,"d":"12.1980"}]
["HMGIY",2,7,15,{"v":11,"d":"11.0"},{"v":7.82905313984415,"d":"7.8291"},{"v":9.00548854378641,"d":"9.0055"},{"v":8.41727084181528,"d":"8.4173"}]
["IRF",7,7,18,{"v":12.7142857142857,"d":"12.7"},{"v":11.000075825885,"d":"11.0001"},{"v":21.5088732717186,"d":"21.5089"},{"v":15.6491001807051,"d":"15.6491"}]
["NFAT",2,10,12,{"v":11,"d":"11.0"},{"v":9.8805541785437,"d":"9.8806"},{"v":10.4339727128014,"d":"10.4340"},{"v":10.1572634456726,"d":"10.1573"}]
["NFkB",7,10,24,{"v":13.4285714285714,"d":"13.4"},{"v":10.8322418622401,"d":"10.8322"},{"v":32.0874600213433,"d":"32.0875"},{"v":16.2242255291795,"d":"16.2242"}]
["PU1",2,8,8,{"v":8,"d":"8.0"},{"v":8.81537798817042,"d":"8.8154"},{"v":11.0129544437438,"d":"11.0130"},{"v":9.91416621595712,"d":"9.9142"}]
["Sp1",6,10,14,{"v":11.6666666666667,"d":"11.7"},{"v":8.90287604497145,"d":"8.9029"},{"v":15.6052176516552,"d":"15.6052"},{"v":11.3709238542828,"d":"11.3709"}]
["Average",{"v":7.636363636363637,"d":"7.6"},{"v":8.090909090909092,"d":"8.1"},{"v":15.636363636363637,"d":"15.6"},{"v":11.510385813017391,"d":"11.5"},{"v":9.174275802583523,"d":"9.2"},{"v":16.973795737080405,"d":"17.0"},{"v":11.746971810167894,"d":"11.7"}]
["Median",{"v":7,"d":"7.0"},{"v":7,"d":"7.0"},{"v":15,"d":"15.0"},{"v":11.6666666666667,"d":"11.7"},{"v":8.90287604497145,"d":"8.9"},{"v":15.6052176516552,"d":"15.6"},{"v":11.6724492225626,"d":"11.7"}]
[]
[null,"The number of PWMs","Size of the smallest",null,"Average size of the","Information content","Information content","Average information "]
[null,"in the equivalence","PWM in each",null,"PWMs in each ","of the PWM in each","of the PWM in each","content of all the PWMs"]
[null,"sets used to represent","equivalence set",null,"equivalence set","equivalence set that","equivalence set that","in the equivalence set"]
[null,"each motif",{"$nulls":3},"has the lowest IC ","has the highest IC ","used to represent"]
[{"$nulls":7},"each motif"]
[]
[]
["Number of PWMs in Transfac PWM sets at different noise levels"]
[]
["Module class","no decoys","50% decoy","75% decoy","90% decoy","95% decoy","99% decoy"]
["AP1-Ets",33,66,132,330,660,774]
["AP1-NFAT",21,42,84,210,420,774]
["AP1-NFkappaB",26,52,104,260,520,774]
["CEBP-NFkappaB",16,32,64,160,320,774]
["Ebox-Ets",26,52,104,260,520,774]
["Ets-AML",16,32,64,160,320,774]
["IRF-NFkappaB",14,28,56,140,280,774]
["NFkappaB-HMGIY",9,18,36,90,180,774]
["PU1-IRF",9,18,36,90,180,774]
["Sp1-Ets",20,40,80,200,400,774]
["Max",33,66,132,330,660,774]
["Min",9,18,36,90,180,774]
["Average",19,38,76,190,380,774]
[]
[{"$nulls":6},"All Transfac matrices"]
[{"$nulls":6},"are used"]
[]
["Number of PWMs in custom sets at different noise levels"]
[]
["Module class","no decoys","50% decoy","75% decoy","90% decoy","95% decoy","99% decoy"]
["AP1-Ets",2,4,8,20,40,743]
["AP1-NFAT",2,4,8,20,40,755]
["AP1-NFkappaB",2,4,8,20,40,750]
["CEBP-NFkappaB",2,4,8,20,40,760]
["Ebox-Ets",2,4,8,20,40,750]
["Ets-AML",2,4,8,20,40,760]
["IRF-NFkappaB",2,4,8,20,40,762]
["NFkappaB-HMGIY",2,4,8,20,40,767]
["PU1-IRF",2,4,8,20,40,767]
["Sp1-Ets",2,4,8,20,40,756]
["Max",2,4,8,20,40,767]
["Min",2,4,8,20,40,743]
["Average",2,4,8,20,40,757]
[]
[{"$nulls":6},"2 custom matrices +"]
[{"$nulls":6},"all Transfac matrices"]
[{"$nulls":6},"except those"]
[{"$nulls":6},"corresponding to the"]
[{"$nulls":6},"real motifs"]
[]
[]
[]
[]
[]
[]
["Muscle and liver regulatory regions dataset "]
[]
["Sequence set","Number of motifs","min TFBS","max TFBS","median TFBS","average TFBS","Sequences","Min seq. length","Max seq. length","Avg. seq. length","Total seq length","Modules","min module size (bp)","max module size (bp)","avg. module size (bp)","Module/background"]
["Muscle",5,2,8,{"v":3,"d":"3.0"},3.5,24,269,1000,{"v":851.125,"d":"851"},20427,24,14,294,{"v":120.45833333333333,"d":"120"},{"v":0.14152836931512214,"d":"0.14153"}]
["Liver",4,2,9,{"v":3,"d":"3.0"},{"v":3.642857142857143,"d":"3.6"},12,943,1000,{"v":995.25,"d":"995"},11943,14,26,176,{"v":111.83333333333333,"d":"112"},{"v":0.11236707694884032,"d":"0.11237"}]
[]
[null,null,"Number of TFBS in","Number of TFBS in","median number of TFBS","average number of TFBS",null,"length of shortest","length of longest sequence"]
[null,null,"the smallest module","the largest module","in the modules","in the modules",null,"sequence in the set","in the set"]
[]
["Muscle PWMs"]
[]
["Motif","binding patterns","size (bp)","Information content (IC)"]
["MEF-2",22,12,{"v":16.90966816,"d":"16.91"}]
["Myf",16,12,{"v":15.914141879,"d":"15.91"}]
["Sp1",12,11,{"v":14.7745578491,"d":"14.77"}]
["SRF",21,13,{"v":14.684951091,"d":"14.68"}]
["TEF",12,12,{"v":15.67777247,"d":"15.68"}]
["Average",16.6,{"v":12,"d":"12.0"},{"v":15.59221828982,"d":"15.6"}]
["Median",{"v":16,"d":"16.0"},{"v":12,"d":"12.0"},{"v":15.67777247,"d":"15.7"}]
[]
[]
[]
["Liver PWMs"]
[]
["Motif","binding patterns","size (bp)","Information content (IC)"]
["CEBP",43,13,{"v":7.116066542,"d":"7.12"}]
["HNF-1",21,13,{"v":15.86416622128,"d":"15.86"}]
["HNF-3",11,11,{"v":12.66705962195,"d":"12.67"}]
["HNF-4",13,13,{"v":15.3343288,"d":"15.33"}]
["Average",{"v":22,"d":"22.0"},12.5,{"v":12.745405296307501,"d":"12.7"}]
["Median",{"v":17,"d":"17.0"},{"v":13,"d":"13.0"},{"v":14.000694210974999,"d":"14.0"}]

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