Figure 2.

Transposon methylation and expression. CG methylation levels of individual TEs plotted against their size (kb) and expression levels (Log2 RPKM (reads per kilobase per million mapped reads)) in FB. A three-dimensional scatter plot is shown from two views. TEs belonging to different classes are displayed as different color dots as indicated. Only TEs with detectable expression levels (RPKM >0) are shown; a total of 1,414 TEs for FB. The plane cut at log2 RPKM = 0 (corresponding to RPKM = 1) was set as a threshold for expressed TEs. The results of a similar analysis conducted on FLM and on TEs with undetectable expression levels are shown in Figure S9 in Additional file 1.

Montanini et al. Genome Biology 2014 15:411   doi:10.1186/s13059-014-0411-5
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