Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Fig 3
Comparison of uni-read and Perm-seq analysis.
(a) Distribution of expression levels of genes with (i) Common peaks; (ii) Common and Perm-seq-only peaks; (iii) Perm-seq-only peaks. (b) Percentage of genes in segmental duplications with (i) Common peaks; (ii) Common and Perm-seq-only peaks; (iii) Perm-seq-only peaks. (c) Histone modification profiles within ± 2000 bps of the summits of the Common, Perm-seq-only, and Perm-seq-exclusive Bcl3 peaks in GM12878 and K562 cells, respectively. (d) Percentages of Perm-seq-exclusive and Common peak sets with the M1 motifs from the de novo sequence analysis of the top 500 Common peaks. Common peak set percentages are replaced by the percentages of occurrences in the subset of the Common peak sets (red circles) that is matched to Perm-seq-exclusive peaks in terms of ChIP signal.