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Fig. 1 | Genome Biology

Fig. 1

From: Global impact of somatic structural variation on the DNA methylome of human cancers

Fig. 1

Genes with altered expression associated with nearby SSV breakpoint by the genomic region window method. a Schematic of the method. For each of several specified genomic region windows in relation to genes (upstream, downstream, or within the gene body), an SSV breakpoint matrix annotates for each sample the presence or absence of at least one SSV breakpoint within the given region. Across samples, the association between expression and SSV breakpoint pattern for each gene is then assessed. b For each of the indicated genomic region windows examined, numbers of significant genes (FDR < 5%), showing correlation between expression and associated SSV event (correcting for sample cancer type), across 2334 cases with WGS and expression data. Numbers above and below zero point of the Y-axis denote positively and negatively correlated genes, respectively. Linear regression models also evaluated significant associations when correcting for both cancer type and gene-level CNA. Genes tested for the given region had at least three cases with SSV breakpoint. c Heat map of significance patterns for genes from b (from the model correcting for both cancer type and CNA). Red, significant positive correlation; blue, significant negative correlation; black, not significant (p > 0.05) or not assessed (less than 3 cases with SSV breakpoint events for given gene in the given genomic region). Genes listed are cancer-related [14,15,16] and with FDR < 1%. d Significance of genes in the present study (2334 cases, best FDR from the following regions: 0–20 kb upstream, 20–50 kb upstream, 50–100 kb upstream, 0–20 kb downstream, 20–50 kb downstream, 50–100 kb downstream, or within the gene body), as compared to their significance in both the previous study utilizing low-pass WGS [3], left, and the previous study of PCAWG high-pass WGS [5]. The X-axis indicates the best FDR for the present study, and the Y-axis indicates the best FDR for the corresponding previous study. Genes in the lower right quadrant reached significance only in the present study. Cancer-related, according to refs [14,15,16]. See also Additional file 1: Figure S1 and Additional files 2, 3, and 4

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