Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Fig 4
Conservation analysis of the common and Perm-seq-exclusive peak sets.
(a) Empirical cumulative distribution functions (CDFs) for average phyloP scores of Usf1 binding sites from the Common and Perm-seq-exclusive Usf1 peaks in GM12878 and K562 cells, respectively. Positive scores indicate conservation and negative scores indicate acceleration. (b) Mean position-specific phyloP scores of the Usf1 binding sites for Common and Perm-seq-exclusive Usf1 peaks in GM12878 and K562, respectively. Shaded areas denote ± one standard error of the mean profile. (c) Pearson correlations between the mean position-specific phyloP scores of the binding sites from the Common and Perm-seq-exclusive peak sets. Purple and red circles indicate that correlations are not significantly different than zero only in GM12878 and in both GM12878 and K562 cells, respectively. (d) Mean position-specific phyloP scores of the Zbtb33 binding sites from the Common and Perm-seq-exclusive Zbtb33 peaks in GM12878 and K562 cells, respectively.