Retrotransposons can mobilize into genic regions. (A) Genes that contain somatic retrotransposon insertions in more than one sample. (B) Empirical cumulative distribution function (ecdf) of gene expression, quantified by RNA-seq by Expectation Maximization (RSEM) values, of genes that contain somatic retrotransposon insertions in a specific sample (red) versus the ecdf of gene expression in genes that do not contain retrotransposon insertions across all other samples (black). (C) Genes that contain somatic retrotransposon insertions in or within 200 bp of exons, 5′, and 3′ UTRs. (D) Gene expression of a selection of genes with somatic retrotransposon insertions; the red dot shows the RSEM value in the particular tumor sample that contained the retrotransposon insertion in that gene, while the gray represents the gene’s expression across all other samples within that tumor type that do not contain a retrotransposon insertion.
