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Fig. 4 | Genome Biology

Fig. 4

From: Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses

Fig. 4

Large gene transcription underlies large, cell type-specific, recurrent aCNAs. A Summed gene expression within a 2 Mb window around each aCNA breakpoint, separated into CNA classes as indicated for RPE1 and BJ cells. B Distances from individual aCNAs to the nearest large or giant gene. Control represents 432 randomly generated genomic coordinates. C Proportion of CNAs with a breakpoint that falls within 1 Mb of large/giant gene. D Schematic of chromosome 7, with position of large (>20 Mb) CNAs found in RPE1 and BJ cells, with replication timing profile, gene expression (each dot indicates location and expression level (RPKM values, mean of three replicates) of an individual gene), location of human chromosome 7 CFSs compiled from the literature, location and expression status of nearby large genes. Zoom of selected portion indicates genomic characteristics and CNA positions in BJ and RPE1 cells. E Schematic indicating positions of aCNAs relative to large genes (with specific examples in RPE1 and summary for all large genes for two cell lines). F Proximity of random control sites or aCNAs to either all human CFS or cell line-specific CFS (RPE1-specific CFS taken from [33], BJ-specific CFS taken from [34]). Statistical tests compare all aCNA classes to in silico control CNAs using a one-way ANOVA Kruskal-Wallis test with post hoc Dunn’s correction

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