Repeat enrichment patterns in mouse cell lines. (a) Combinatorial patterns of repeat enrichment in mES cells. The repeat types (rows) were clustered according to the MLE enrichment in different marks (disregarding depletion; see Materials and methods), with red colors corresponding to enrichment, and blue colors corresponding to depletion. Repeat types that do not show statistically significant enrichment or depletion are shown in white. Prominent sets of repeat types are highlighted on the left-hand side (1 to 4; see text). The bottom part of the plot is omitted as it contains repeats devoid of enrichment in any examined modifications. See Figure S5 in Additional file 1 for a complete, magnified view showing all the repeat type labels. (b) An enlarged view of a portion of set 1, illustrating ERV1/ERV-K repeats enriched for H3K9me3 and H4K20me3. (c) A portion of set 2 showing enrichment for H3K4me3 and H3K27me3 at tRNA repeats.