Comparison of uni-read, CSEM, and Perm-seq analysis.

<p>(a) Comparison of Ctcf optimal peak lists from uni-read, CSEM, and Perm-seq analyses. Numbers in parentheses denote comparisons of the optimal peak lists with the relaxed peak lists. For example, there are 1320 peaks identified by the Perm-seq and CSEM analyses and missed by the uni-read analyses. 664 of these peaks are still missed by the uni-read analysis even if we consider comparison of the Perm-seq and CSEM optimal peak lists with the uni-read relaxed lists. (b) Circos plots of CSEM (left) and Perm-seq (right) read allocation for reads mapping to four segmental duplication regions with coordinates chr1:143,880,003–143,978,943, chr1:206,072,707–206,171,611, and chr1:143,880,003–144,005,301, chr1:120,872,119–249,250,621. (c) Percentages of Perm-seq specific and CSEM specific peaks with the most significant motifs identified from the <i>de novo</i> sequence analysis of the intersection peaks, i.e., peaks common to uni-read, CSEM, and Perm-seq analysis. (d) Comparison of the Ctcf peak sets from GM12878 between Perm-seq, CSEM, Gibbs-based [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004491#pcbi.1004491.ref002" target="_blank">2</a>], and Lonut [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004491#pcbi.1004491.ref004" target="_blank">4</a>]. x.vs.Perm-seq denotes optimal peaks of method “x” not identified by Perm-seq. Similarly, Perm-seq.vs.x denotes optimal peaks of Perm-seq not identified by method “x”. (e) Annotation of the K562 peaks with respect to segmental duplications. Categories are: Prom.Dup: peaks that are in promoter regions (± 2500 bps of TSS) of RefSeq genes that reside in segmental duplications; Prom: Peaks in promoter regions (excludes peaks in Prom.Dup); Genic.Dup: peaks that are within [-10000 bps of TSS, +1000 bps of TES] of RefSeq genes that are in segmental duplications (excludes peaks in Prom.Dup); Genic: peaks that are within [-10000 bps of TSS, +1000 bps of TES] of RefSeq genes (excludes peaks in Genic.Dup, Prom.Dup); Dup: peaks that are in segmental duplications (excludes Prom.Dup and Genic.Dup); None: peaks that do not fall into any of the other defined categories. (f) Genes are ordered with respect to RNA-seq transcripts per million (TPM) values. Genes with a Common Pol2 peak in their promoters are depicted with green whereas genes with only Perm-seq-only peaks are depicted in blue.