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Fig. 5 | Genome Biology

Fig. 5

From: Comparison of computational methods for the identification of topologically associating domains

Fig. 5

Assessment of TAD calling with biological features. a Schematic representation of the structural proteins CTCF (orange), RAD21 (blue), and SMC3 (red) that are enriched at TAD boundaries. b, c Representative examples of ChIP-seq peak signals (average number of peaks in 5-kb intervals) for TopDom (b) and spectral (c). Peak signals for CTCF (orange line), RAD21 (blue line), and SMC3 (red line) are overlaid. d Fold change of structural protein peak signals at TAD boundaries for CTCF (orange bar), RAD21 (blue bar), or SMC3 (red bar). TAD callers are ordered from left to right by increasing average fold change of peak signals of the three proteins. The fold change was computed as the ratio of protein binding signal at TAD boundaries (upper-left, red area) versus flanking regions (upper left, gray areas) minus 1. e Fold change of CTCF peak signal for boundaries called by at least 50% of the callers (red bars) or less than 50% of the callers (blue bars). f Mean fold change across callers of CTCF peak signal for shared (red track) and not shared (blue track) boundaries as a function of the minimum number of callers to define shared boundaries. Error areas correspond to one standard deviation. g CTCF fold change vs TAD mean size for each hierarchy level of the different callers. Hierarchical levels are labeled by increasing numbers (L1, …, Ln) with L1 being the level including TADs that do not contain nested TAD. Overall Pearson’s correlation = 0.37, Pearson’s correlation within the window [250–1250 kb] (gray area) is 0.05. The size of the dots is proportional to the number of TADs. h Schematic representation of H3K36me3 (green) or H3K27me3 (red) histone mark ChIP-seq read counts observed within TADs: TADs are typically enriched either for H3K36me3 marks (example of the left) or for H3K27me3 marks (example on the right) in a mutually exclusive manner. i For each TAD caller, fraction of TADs with a significant (high or low) H3K27me3/H3K36me3 log10-ratio (FDR < 0.1)

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