Table 6.

Comparison of ranked target lists between the 50 b every 50-b array and ChIP-PET platforms

Comparison of the ranked target list for the top 75 targets from the 50 b every 50-b array data set and 75 PET3+ targets from the ChIP-PET experiment. A fair evaluation could only be made for the 75 PET3+ clusters that were covered by the 50 b every 50-b array tile path (Supplemental Table 1). (A) The upper panel displays the false-positive rates (FPR) calculated for each data set considered separately. (B) The lower panel displays the results after merging the list of the top 75 targets identified by the 50-b arrays with the 75 PET3+ targets identified by ChIP-PET. Additionally, the ChIP-PET targets are all sized to be 1300 bp (centered on the overlap region) in order to perform a fair comparison. As for Table 1, this comparison is performed by first creating the union of the two separate lists and then counting the number of union target regions specific to either the 50-b array targets or the PET3+ clusters, or those targets identified by both platforms. In each of these three categories, the union regions that were tested for validation are displayed as well as the associated false-positive rate.