Table 3. p-values for associations between gene expression and gene classification.
| Expression Value | Peak Location | FindPeaks | PeakSeq | USeq | MACS |
| High | Downstream | 1.00 | 1.00 | 1.00 | 1.00 |
| High | None | 0.00 | 1.00 | 0.00 | 0.00 |
| High | Upstream | 0.98 | 1.00 | 1.00 | 1.00 |
| High | Within | 1.00 | 0.00 | 0.66 | 1.00 |
| Low | Downstream | 0.65 | 0.00 | 0.00 | 0.00 |
| Low | None | 1.00 | 0.00 | 1.00 | 1.00 |
| Low | Upstream | 0.00 | 0.00 | 0.00 | 0.00 |
| Low | Within | 0.00 | 1.00 | 0.17 | 0.00 |
| Middle | Downstream | 0.00 | 0.73 | 0.22 | 0.59 |
| Middle | None | 1.00 | 0.94 | 0.52 | 0.13 |
| Middle | Upstream | 0.72 | 0.84 | 0.47 | 0.67 |
| Middle | Within | 0.02 | 0.02 | 0.70 | 0.80 |
This table shows the results of using a hypergeometric test to test for statistical significance between the expression value for genes and the peak classification for genes. The expression value and peak location indicate the classification of the genes for expression and peak classification, respectively. The remaining four columns provide the calculated p-values based on peak classifications for each of the peak identification programs. The statistically significant cells are bold. A cut-off of 10−2 was used to identify significant relationships.