Table 3 |
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|
The effect of truncating the sequence upstream of the TSS |
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|
Sequence range |
TSS Tompa Dataset |
TRANSFAC Dataset |
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|
|
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|
Without positional info |
With positional info |
p-value |
Without positional info |
With positional info |
p-value |
|
|
|
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|
[-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 |
|
|
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|
The first column shows the sequence range upstream of the TSS given as input to A-GLAM. 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 p-value, 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 p-value of 0.054. To view results for individual sites in the Tompa dataset, see Supplementary Table 7 [see Additional file 1]. |
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|
Kim et al. BMC Bioinformatics 2008 9:262 doi:10.1186/1471-2105-9-262 |
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