Supplementary Figure 8: Analysis of footprint ranking strategies.
From: Analysis of computational footprinting methods for DNase sequencing experiments
Distribution of AUC values (at 10% FPR) by using distinct ranking strategies for site centric methods: (a) BinDNase, (b) Centipede, (c) Cuellar, (d) FLR, (e) PIQ and (f) segmentation methods DNase2TF and Wellington. Ranking strategies (x-axis) are ranked by decreasing median AUC. The site-centric methods are tested based on probability (P) cutoffs of 0.8, 0.85, 0.9, 0.95, 0.99 and their own ranking strategy (Own rank). Segmentation methods are tested based on the TC metric ranking and their own ranking strategy (Own rank). Methods not shown in this figure do not contain an intrinsic ranking methodology. In all cases, using TC-based strategies/cutoff was significantly better than the original ranking of the methods (p-value < 10−12; Mann-Whitney-Wilcoxon test). Concerning site-centric methods, the use of a probability threshold (P) of 0.9 was best for all methods, with the exception of BinDNase, where 0.8 was best. The box plot depicts the distribution median value (middle dot) and first and third quartiles (box extremities). The whiskers represent the 1.5 IQR and external dots represent outliers (data greater than or smaller than 1.5 IQR).
