Fig. 3

The comparison of SpectralTAD and other TAD callers regarding TAD consistency and biological significance. To test for robustness to noise, sparsity, and sequencing depth, TADs were called from simulated Hi-C matrices using SpectralTAD and four other TAD callers. They were compared with the ground-truth TADs using the Jaccard similarity metric. The performance was assessed at different levels of noise (a), sparsity (b), and downsampling (c, see Methods). Using the raw data from GM12878 at 25 kb resolution, enrichment of genomic annotations within 50 kb regions flanking a TAD boundary on both sides was assessed using a permutation test. The average number of annotations for enriched (d) and depleted (e) genomic features and the permutation p-values corresponding to enrichment (f), and depletion (g) for the top five most enriched/depleted genomic annotations are shown. Results averaged across chromosome 1–22 are shown