Skip to main content
Figure 3 | BMC Bioinformatics

Figure 3

From: A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data

Figure 3

Comparison of HPeak and the proposed algorithm in detecting regions on the prostate PolII ChIP-seq data (parameters of 25 bp for bin size, 0.01 for FDR and 6.5 for Peak-to-threshold ratio). The bin size is the same between the two algorithms. A: A region detected using the proposed algorithm but not by HPeak. Top: the original histogram of the ChIP-seq data. Bottom: the NL-means filtered data and the detected regions (marked by the red bar). The length of the detected region (10375 bp) is marked under the red bar. A gene (NEAT1, marked by black bar) is covered by this region. B: Another region detected using the proposed algorithm but not by HPeak. Top: the original histogram of the ChIP-seq data. Bottom: the NL-means filtered data and the detected regions (marked by the red bar, 2975 bp long). A snoRNA gene (U5E) and its pseudogene (marked by black bars) are covered by this region. C: Two regions detected by HPeak but not the proposed algorithm. The HPeak detected regions are marked using green bars (the lengths are 675 bp and 200 bp, respectively). We examined all regions that were missed by the proposed algorithm under this set of parameters, all regions contain short spike-like peaks as shown here.

Back to article page