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. 2016 Jul 19;44(20):9624–9637. doi: 10.1093/nar/gkw633

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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — RAG1 peaks segregate into two clusters. (A) Hierarchical clustering of RAG1^hi H3K4me3 peaks according to peak-specific feature importance. Each column represents a RAG1^hi peak and each row represents a feature. Feature importance is color coded. Dendrogram above the heat map represents the hierarchical clustering of the peak set. (B) Boxplots of the levels of each feature in RAG1^hi promoter (orange; N = 2368) and enhancer (purple; N = 307) clusters (filled boxes) compared with RAG1^lo regions (empty boxes; 1407 promoters and 1454 enhancers) selected to be comparable for certain ‘fixed’ parameters, as indicated by red boxes. (C and D) Snapshots of representative RAG1^hi versus RAG1^lo (C) promoters and (D) enhancers illustrate the levels of WT RAG1, H3K4me3, H3K27Ac and DNaseI-HS. The numbers in parentheses indicate the maximal RPKM.