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Fig. 8 | Genome Biology

Fig. 8

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

Fig. 8

Applying GRiNCH to datasets from different 3D genome conformation capture technologies. Visual comparison of the interaction profile and GRiNCH TADs from a 8Mb region in chr8, GM12878 cell line. GRiNCH TADs are visualized as blocks of different colors under the heatmap of interaction counts. A Hi-C vs SPRITE. The top heatmap and clusters are from Hi-C; bottom from SPRITE. B HiChIP with cohesin (top) vs HiChIP with H3k27ac (bottom). C Hi-C (top) vs HiChIP with cohesin (bottom). D Hi-C (top) vs HiChIP with H3K37ac (bottom). For visualization purposes all interaction counts were log2-transformed. E Measuring the similarity of GRiNCH TADs from Hi-C and other 3D genome conformation capture platform (e.g., SPRITE, HiChIP with cohesin, or HiChIP with H3k27ac) in the same GM12878 cell line, with Rand index. The dendrogram depicts the relative similarity between samples. F Mutual information-based similarity of GRiNCH TADs from Hi-C and other technologies

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Genome Biology

ISSN: 1474-760X

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