SVExpress is a suite of computational tools (implemented in Excel VBA and R) that allows one to identify Structural Variant (SV) breakpoint-to-expression associations across a set of cancer samples profiled for both SVs and gene transcription. SVExpress takes as input a table of somatic SV breakpoints and a gene-to-sample expression matrix. SVExpress then constructs a gene-to-sample breakpoint matrix, which the user can then integrate with corresponding expression data by linear regression modeling. Furthermore, using SVExpress, top SV-gene associations identified can be examined in terms of enhancer hijacking or disruption of TADs.