Fig. 5

Evaluation of SVExpress results in the context of SV-HotSpot and cis-X SV analysis tools. a From results using the CCLE datasets, Venn diagram represents the overlap between the genes significantly correlated with SV breakpoint by SVExpress (FDR < 10%, using 1 Mb region window and correcting for cancer type and CNA) with the set of genes associated with nearby SV hotspot peaks by SV-HotSpot [7]. P-value by one-sided Fisher’s exact test. Genes listed, involving the overlap between the SVExpress and SV-HotSpot results sets, also have a previous cancer association by COSMIC [23]. b Survey of SV hotspot peaks across chromosome 2, by genomic position. SV-HotSpot uses a default threshold of 10% of cell lines for calling SV hotspot peaks. Along the top of the plot, the genomic positions of the genes significant by SVExpress are represented. Asterisks indicate significant SVExpress genes that also are associated with an SV-HotSpot peak. c For cancer cell lines with SV breakpoint within 500 kb of MYCN, allele-specific patterns associated with increased expression. P values by binomial test using cis-X [6]