Fig. 1: Structural Variant (SV) breakpoints associated with altered expression of nearby genes.

a Numbers of SV breakpoints identified as occurring within a gene body, 0–20 kb upstream of a gene, 20–50 kb upstream of a gene, 50–100 kb upstream of a gene, or 0–20 kb downstream of a gene. For each SV set, the breakdown by alteration class is indicated. SVs with breakpoints located within a given gene are not included in the other upstream or downstream SV sets for that same gene. b For each of the SV sets from part (a), numbers of significant genes (p < 0.001, FDR < 4%), showing correlation between expression and associated SV event. Numbers above and below zero point of y-axis denote positively and negatively correlated genes, respectively. Linear regression models also evaluated significant associations when correcting for cancer type (red) and for both cancer type and gene copy number (green). c Heat map of significance patterns for genes from part (b) (from the model correcting for both cancer type and gene copy number). Red, significant positive correlation; blue, significant negative correlation; black, not significant (p > 0.05); gray, not assessed (<3 SV events for given gene in the given genomic region). d Significantly enriched Gene Ontology (GO) terms for genes positively correlated (p < 0.001 and FDR < 4%) with occurrence of SV upstream of the gene (for either 0–20 kb, 20–50 kb, or 50–100 kb SV sets). P-values by one-sided Fisher’s exact test. e Patterns of SV versus expression for selected gene sets from part (d) (telomerase holoenzyme complex, top; eukaryotic translation initiation factor 2B complex, middle; insulin receptor binding, bottom). Differential gene expression patterns relative to the median across sample profiles. See also Supplementary Data 1, 2 and Supplementary Fig. 1.