Fig. 5

TE insertions associated with cellular phenotypes. a. Associations with DNA methylation. (Upper panel) Diagram of the SS18L1 (Synovial sarcoma translocation gene on chromosome 18-like 1) gene locus, which contains an antisense Alu associated with increased CpG methylation at that gene (i.e., in cis, p = 3.67x10^-6) (Middle panel) Manhattan plot showing TE positions on the x-axis and strengths of association with gene methylation on the y-axis (Bonferroni-corrected p-values). Singleton insertions were excluded from association analyses. Gene abbreviations are given for both the gene in which the insertion is found (red) and the associated methylation site (black) in examples. The TE insertion at the CSRP2 (cysteine and glycine-rich protein 2) gene locus was associated with methylation at 22 distinct loci (Lower panel). The associated methylation sites are distributed throughout the genome. b. Manhattan plot showing associations with steady state mRNA levels. Gene abbreviations are given for both the gene in which the insertion is found (red) and the associated transcript level (black); in these two examples, the TE is associated with upregulation of the mRNA. c. Manhattan plot showing associations with drug sensitivity as measured by total cellular growth inhibition. The gene in which the insertion is found is given (red), as well as the associated pharmacologic agent (black)