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Fig. 6 | Genome Biology

Fig. 6

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

Fig. 6

TAD caller performance across independent datasets. a, b Mean size of the TADs identified in the GM12878 Hi-C dataset (X-axis) versus the mean size of the TADs identified in four Hi-C datasets (Y-axis): GM12878 replicate 1 (dark blue), GM12878 replicate 2 (light blue), IMR90 (green), mouse cortical neurons (MNC, red). Results are shown for 6 TAD callers and Hi-C matrices using 10-kb bin size (a) and 50-kb bin size (b). For some of the TAD callers, jitter on the X-axis was added to improve visibility of the dots; the gray thin lines indicate the TAD mean size values in the GM12878 dataset. c Measure of Concordance (MoC) between TAD partitions determined by all pairs of callers (among the 6 tested—see panel a) in the GM12878 dataset (X-axis) and the other tested datasets (Y-axis). Results for each of these datasets are shown in distinct subplot; datasets are labeled and color-coded. d, e CTCF binding fold change (d) and ratios between H3K27me3 and H3K36me3 within TADs (e) obtained by the TAD callers for the GM12878 dataset (X-axis) versus and the corresponding values obtained in the four tested datasets (Y-axis, color-coded as in panels a and b). For some of the TAD caller, jitter on the X-axis was added to improve visibility of the dots; the gray thin lines indicate the TAD mean size values in the GM12878 dataset

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