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Fig. 4 | Genome Biology

Fig. 4

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

Fig. 4

Pairwise comparison of TADs identified by all TAD callers (ICE-normalized Hi-C data at 10-kb resolution). a Histograms of the numbers of unique TAD boundaries (start and end positions of each TAD) identified by a given number of TAD callers (on the rows) with an increasing tolerance radius ranging from 0 (± 0 kb) to 5 bins (± 50 kb). b Histograms of the numbers of TADs identified by a given number of TAD callers (on the rows) with an increasing tolerance radius ranging from 0 (± 0 kb) to 5 bins (± 50 kb) for each TAD boundary. c Fraction of TAD boundaries identified by each TAD caller (rows) that were also identified by 5 or less (blue), between 6 and 10 (green), between 11 and 15 (orange), and more than 15 (red) other TAD callers. d Fraction of TADs identified by each TAD caller (rows) that were also identified by 1 (blue), between 2 and 5 (green), between 6 and 10 (orange), and more than 10 (red) other TAD callers. e Average Measure of Concordance (MoC) between TADs identified by each caller (rows) versus TADs identified by all other callers. TAD callers are annotated by the general approach they adopt (colored dots) and ranked (from top to bottom) by decreasing average MoC. f Map of the t-SNE analysis performed on the Pearson’s correlation matrix of the matrix of pairwise MoC between TADs identified by all callers. TAD callers are annotated by the general approach they adopt (colored dots). Three clusters were manually annotated, and the mean MoC within and between each of these groups is reported. ClusterTAD and PSYCHIC were not included in any of the clusters as their MoC values with each member/most members of closest group were below the average of the group. g Boxplot of the number of TADs detected by the callers in each of the three groups identified from the t-SNE analysis

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