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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

Identification of topologically associating domains (TADs) in chromosome 6 of the GM12878 cell line from ICE-normalized Hi-C data. a The performance of 22 TAD callers (listed on the left and right) was assessed using Hi-C data of the chromosome 6 of the lymphoblastoid cell line GM12878. b Total number of TADs detected in the ICE-normalized Hi-C data of chromosome 6 at four different resolutions (10, 50, 100, 250 kb) by each of the 22 TAD callers. Color intensity is proportional to the number of TADs in log-scale, and gray boxes correspond to TAD callers that did not successfully identified TADs at a given resolution. c Mean size (measured in kb) of the TADs detected in the ICE-normalized Hi-C data of chromosome 6 at four different resolutions (10, 50, 100, 250 kb) by each of the 22 TAD callers. Color intensity is proportional to the mean size of the TADs in log-scale, and gray boxes correspond to TAD callers that did not successfully identified TADs at a given resolution. d, e Variation of the mean size of the TADs measured in kb (d) or in number of bins (e) across Hi-C matrix resolutions. Each line refers to a TAD caller (numbered as indicated at the bottom of the plot), and only TAD callers that successfully identified TADs at all five resolutions are shown. f Slopes derived from the linear fit of the curves in panel d (TAD size in kb across resolutions) versus slopes derived from the linear fit of the curves in panel e (TAD size in number of bins across resolutions). Dots are colored based on the general approach used by the tool (“linear score,” “clustering,” “statistical model,” “network features”—see Table 1). The dashed line indicates the linear fit

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