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Fig. 6 | Genome Biology

Fig. 6

From: A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

Fig. 6

Conservation and divergence of Arboretum-Hi-C clusters of human and mouse ESCs. a On the left is a heat map of different regulatory features enriched in human ESC, reordered according to the Arboretum cluster assignments, and on the right is the heat map of − log10 of KS test P values (like Fig. 2). b The same as (a) for mouse ESC. c Heat map of overlap between clusters of human and mouse ESCs. The off-diagonal elements are highlighted based on the type of divergence (between clusters of the same activity level or between clusters of different activity levels). d Example of module divergence between C9 and C0 in human and mouse ESCs. (i) Heat map of Spearman’s correlation of contact counts for the regions that are in C9 or C0 in human and mouse ESC lines. Solid lines show the demarcation of regions that are in the same cluster in both human and mouse, while dashed lines show regions that have switched clusters between C9 and C0 in human and mouse. (ii) Box plots of distribution of correlation from 29 diverged regions to the regions that stay in C9 and C0 in both human and mouse. e Distribution of (i) LADs, (ii) DNase I peaks, and (iii) number of genes in regions that are conserved or switch between clusters. (i) The first three box plots for LADs show human regions that remain C9 in both human and mouse (hESC_9 mESC_9), regions that switch from C9 to C0 (hESC_9 mESC_0), and the regions that are in C0 in both human and mouse (hESC_0 mESC_0). The remaining three box plots shows the LAD distribution in mouse ESC for regions that remain in C9 in both human and mouse, the regions that have switched to C0, and finally, those that remain in C0 in both. (ii) and (iii) are the same as (i), showing DNase I and number of genes. f Like d for the regions that diverge between C1 and C9 in human ESC and IMR90 cells. g Like e, showing the distribution of RAD21 and CTCF peaks in regions exhibiting the same and difference cluster assignments in hESC and hIMR90. ESC embryonic stem cell, hESC human embryonic stem cell, hIMR90 IMR90 human fibroblast, LAD lamina-associated domain, mESC mouse embryonic stem cell

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