Fig. 4

TE enrichment analyses. a. STOP and GO genes have been implicated in breast cancer as genes that appear to inhibit and promote tumor development, respectively. Using a hypergeometric distribution to assess enrichment, we found that TE insertions are enriched in STOP genes on the array (p = 1.23x10^-9) but not in GO genes (p = 0.33). b. The bar graph shows enrichment by type of TE plotted as the negative log of the p-value. No GO gene enrichment is seen. STOP gene enrichment is seen considering all LINE-1 (p = 3.11x10^-3); all Alu (p = 2.27x10^-10); as well as LINE-1 singletons (p = 4.16x10^-5). c. Insertions were also enriched in common insertion sites (CIS) (p = 1.46x10^-4); COSMIC commonly mutated cancer genes (p = 7.74x10^-10); and genes reported to acquire somatic LINE-1 insertions in cancer by Lee et al. (p = 5.34x10^-14). d. Genes with TE insertions in ovarian cancer cell lines are more likely than other genes to be downregulated in ovarian cancer samples as compared to normal tissue controls. Randomly selected genes are shown for comparison (bottom panel)