Figure 6

Primate-specific L1 elements are overexpressed in a subclass of patients with more advanced tumor progression. (A) Clustering of log2 expression fold-changes in the subset of primate specific L1s that showed significant differential expression reveals two major classes of patients (Group 1 and Group 2). Group 1 shows widespread overexpression of primate specific L1s and contains patients with more advanced tumor progression. The number of somatic insertions refers to the number of previously reported somatic retrotransposition events for that L1 subfamily identified in prostate cancer [26]. (B) All L1 sequences in the human genome were fetched and mapped to L1Hs consensus using permissive, local alignment parameters to analyze data. Using this distribution we computed the cumulative distribution of start and end positions of genomic L1s with respect to the consensus to describe the background distribution of L1s that can potentially map to the consensus element. (C) Coverage of L1 sequences in prostate tumor versus normal RNA-seq that map to L1Hs consensus using a local alignment (Bowtie2). The log2FC was computed for each position along the L1Hs consensus from tumor and normal-matched RNA-seq coverage. Hierarchical clustering was done based on the log2FC using Euclidean metrics.