Skip to main content
Fig. 2 | Genome Biology

Fig. 2

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

Fig. 2

Characterizing TADs with internal validation metrics, TAD size, and composition. A Percentage of TADs with significant Davies-Bouldin index (DBI) and Delta Contact Count (DCC) values. Shown are values for GRiNCH and six other methods. The higher the bar, the better a method. Note: 3DNetMod outputted overlapping TADs and was excluded from this analysis which involves TAD shuffling. B The size distribution of TADs from GM12878. Y-axis is in log10 scale of base pairs. The white dot represents the median; the black box ranges from the 25th percentile to 75th. 10kb data from insulation is missing because it did not return any TADs when using the same hyperparameters as in 25kb and 50kb data. C Similarity between TADs from higher- and lower-resolution data (e.g., 10kb vs. 25kb) measured by Rand index. The higher the number, the higher the similarity. The error bar denotes the standard deviation from the mean across chromosomes. Note: 3DNetMod outputted overlapping TADs and was excluded from this analysis due to the requirement of unique cluster assignment for each region

Back to article page

Genome Biology

ISSN: 1474-760X

Contact us