Fig. 7

Gene signatures and pathways associated with the overall burden of structural variation across cancers. a Across the 2334 cases with both WGS and RNA-seq data, heat maps of gene expression-based signatures scoring for DNA damage response pathways [30], methylation (by Gene Ontology or GO categories), and immune cell infiltrates [31]. Gene signature scores are the average of normalized expression values (for immune signatures, expression values normalized within each cancer type; for other signatures, expression values normalized across sample profiles). p values by linear model correcting for both cancer type and low-pass versus high-pass WGS. b Diagram of key genes involved with DNA double-strand break repair pathway, with corresponding correlation with the overall structural variation burden (red, significantly higher with increasing number of SSVs). c Similar to b, with diagram of key genes involved in methylation of DNA and histones. d Similar to b, with diagram of immune cell types and associated gene markers. FDR values in b and c (based on the entire set of 17,798 genes profiled) by linear model correcting for both cancer type and low-pass versus high-pass WGS