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Fig. 1 | BMC Bioinformatics

Fig. 1

From: SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints

Fig. 1

Workflow diagram for the SVExpress suite of computational tools. SVExpress identifies SV breakpoint-to-expression associations across a set of cancer samples profiled for both SVs and gene transcription. Initially, SVExpress takes as input a table of SV breakpoints (which may be generated using any standard SV calling algorithm) and a set of gene coordinates. SVExpress then constructs a gene-to-sample breakpoint matrix using an Excel macro (“Generate_Gene_to_Sample_SV_Table”). The user can then take this breakpoint matrix and integrate it with the corresponding matrices for gene expression and gene-level copy number alteration (CNA) by linear regression modeling using the provided R code. This code generates p values and t-statistics for each gene, associating SV breakpoint pattern with expression, with or without correcting for CNA. Furthermore, using SVExpress Excel macros, a set of SV-gene associations identified can be examined in terms of enhancer hijacking (e.g., an enhancer represented by one breakpoint positioned in proximity to a gene nearby the other breakpoint) or in terms of disruption of TADs. SVExpress carries out the above using the "Generate_SV_to_Enhancer_Associations" and "Generate_SV_to_TAD_Associations" macros, respectively. SV, Structural Variant; CNA, copy number alteration; TAD, topologically associated domain

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