Fig. 5

Refinement and analysis of the 16p11.2 RER region in breast cancer cell lines. a Black bars indicate genes along 16p11.2, oriented from centromere (top) to telomere (bottom), which have significant TCSs at varying window (2n + 1) size with n from 1 to 10. Gene expression data are from tumor cell lines [20]. Gene names are listed to the right, as are the position of fluorescence in situ hybridization (FISH) probes that were used to examine the four RER subregions. b Box plots show the distribution of normalized FISH interprobe distances (d ² /r ²) [31, 32] measured across the four subregions of the 16p11.2 RER region in MCF7 and MDAMB231 breast cancer cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1). c Unsupervised cluster analysis of gene expression z scores for subregion 2 in 48 breast cancer cell lines (red ER−, blue ER+) [20]. Cell line names are indicated along the bottom of the heat map. Red/green z scores equate to increased/decreased gene expression, respectively. Genes are ordered by their position on the chromosome and listed to the right. The yellow boxes indicate cell lines examined by FISH. d Example FISH images using probe pairs (red and green) that delineate subregion 2 (as in (a)) in ER+ cell lines MCF7 and LY2 (upper panels), and ER− cell lines MDAMB231 and MDAMB468 (lower panels). DNA is stained with DAPI (blue). Scale bar = 5 μm. The boxplots to the right show the distribution of normalized FISH interprobe distances (d ² /r ²) across subregion 2 in the four cell lines. n = 45–60 nuclei. The significance of differences between datasets was assessed by Wilcox test (Table S3 in Additional file 1)