Abundance of cancer-specific LTR element–overlapping transcripts. (A) Total number of CLTs identified per cancer type. (B) Overlap of CLT expression between cancer types, plotted as the number of CLTs against the number of cancer types sharing a given CLT. (C) Heatmap of expression values in cancer patient and healthy control samples of all 5923 identified CLTs (top), KIRC-specific and KIRP-specific CLTs (570) (middle), and SKCM-specific and UVM-specific CLTs (891) (bottom). (D) Proximity, in nucleotides, of the identified CLT TSS to ATAC-seq peaks. Also shown is the proximity of ATAC-seq peaks to the center of 10 random sets of similar numbers of LTR elements. (E) Composition of identified CLTs according to the indicated position of the LTR element in the transcript structure.
