Sequence range

TSS Tompa Dataset

TRANSFAC Dataset



Without positional info

With positional info

pvalue

Without positional info

With positional info

pvalue

[2000, 0]

0.008

0.101

0.002

0.009

0.027

10^{8}

[1000, 0]

0.086

0.098

0.583

0.050

0.066

0.112

[500, 0]

0.125

0.133

0.338

0.077

0.078

0.070

[250, 0]

0.139

0.139

0.054

0.094

0.076

0.603

 The first column shows the sequence range upstream of the TSS given as input to AGLAM. The change of CCC from modes with and without positional information for the TSS Tompa and TRANSFAC datasets is displayed in the corresponding groups of three columns. The third column of each group shows a Wilcoxon pvalue, which evaluates the difference between the CCCs in the previous two columns. Because not all TFBSs in our datasets are known, small improvements in the CCC correspond to true improvements of unknown magnitude. In particular, e.g., in the Table, two CCC values rounded to 0.139 have unseen decimals different enough to have a pvalue of 0.054. To view results for individual sites in the Tompa dataset, see Supplementary Table 7 [see Additional file 1].