Figure 7

Comparison with other computational tools for analyzing PAR-CLIP data. The reliable target gene lists for EWSR1 and FUS proteins were obtained from an independent study [36] and used as a standard for comparison of different computational tools. Cross-linking regions are sorted according to the read counts in that region, and the top 1,000, 2,000, and 5,000 regions were selected as the candidate binding regions from each computational method. The percentage of coverage (y-axis in the figure) was defined as the ratio of the number of selected cross-linking regions that were covered in the reliable gene regions (5' UTR to 3' UTR of a gene in the reliable target list) compared to the number of selected cross-linking regions that were covered in the 5' UTR to 3' UTR of any genes in the genome. We calculated the percentages of coverage for PIPE-CLIP, Piranha, PARalyzer and MACS2 for both EWSR1 and FUS proteins.