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Fig. 5 | Genome Biology

Fig. 5

From: GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

Fig. 5

Evaluating TAD-calling methods with enrichment of boundary elements and regulatory signals. A Fold enrichment of binding signals of architectural protein in TAD boundaries. Shown are the mean fold enrichment of CTCF ChIP-seq peaks and accessible motif instances of cohesin proteins, RAD21 and SMC3, estimated across multiple chromosomes. The error bar denotes the standard deviation from the mean. B Proportion of TADs with significant mean histone modification signal (i.e., empirical p-value <0.05). The darker the entry the higher the proportion of TADs with significant histone enrichment. The average ChIP-seq signal for each histone modification mark was taken from within each TAD; the p-value of each TAD is derived from an empirical null distribution of mean signals in randomly shuffled TADs. Note: 3DNetMod outputted overlapping TADs and was excluded from this analysis as it involves TAD randomization/shuffling

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Genome Biology

ISSN: 1474-760X

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