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. 2019 Dec 10;10:5640. doi: 10.1038/s41467-019-13555-x

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a For all individual TEs in each class, the total number of chromHMM states the TE is annotated with across all epigenomes (DNA n = 456,948 TEs, LINE n = 1,480,369, LTR n = 708,210, SINE n = 1,769,839, SVA n = 3,608, Other n = 11,814). b For all individual TEs in each class, the total number of methylation states the TE is annotated with across all epigenomes (TEs overlapping CpGs only: DNA n = 275,140 TEs, LINE n = 952,459, LTR n = 532,571, SINE n = 1,430,171, SVA n = 3,519, Other n = 6,568). a, b Histograms are colored by class (facet). c For TEs in chromHMM State 1 in at least one Roadmap epigenome (see Fig. 2a, red dots), the average proportion of epigenomes in which they are annotated with chromHMM State 2 (represented by color scale below c, d, 0 to 100% of epigenomes). d For TEs in methylation State 1 in at least one Roadmap epigenome (see Fig. 2a, red dots), the average proportion of epigenomes in which they are annotated with methylation State 2 (represented by color scale below c, d, 0 to 100% of epigenomes).