Figure 1: Analysing aneuploidy and large CNAs in breast cancer GEMMs using gene expression profiles. | Nature Communications

Figure 1: Analysing aneuploidy and large CNAs in breast cancer GEMMs using gene expression profiles.

From: The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis

Figure 1

(a) A representative example of gene expression-based CNA analysis. Left: moving average plots of global gene expression levels along the genome of five normal mammary samples (blue lines) and five tumour samples (brown lines) from the p53−/− model. Right panel: piecewise constant fit (PCF) detection of CNAs in the same samples based on coordinated deviations of gene expression levels throughout large genomic regions. Amplifications are shown in red, deletions in blue. (b) A pie chart describing the 2,697 gene expression profiles analysed: 567 normal tissue samples, 100 premalignant mammary tissues/lesions, 1,910 primary mammary tumours, 17 breast cancer metastases, and 103 breast cancer cell lines and cell line-derived tumours. These data were collected from 36 unique breast cancer mouse models. Letters represent normal tissues: a, non-mammary tissues from transgenic mice; b, mammary tissues from female control mice; c, non-mammary tissues from control mice; and d, mammary tissues from female transgenic mice. Roman letters represent cell lines and tumours derived from them: I, established breast cancer cell lines; II, cell line-derived tumours; and III, freshly derived cell lines. Tumours from GEMMs with >20 samples are presented by name, and numbers represent tumours from the remaining GEMMs: 1, Igf1r; 2, Apc+/−; 3, Pten−/− p53−/−; 4, Hras; 5, Brg+/−; 6, Brca2−/−; 7, Stat5−/−; 8, Wnt Fgfi; 9, DMBA; 10, p53+/− IR; 11, Rb−/−; 12, Int3/Notch4; 13, Brca1+/− p53+/− IR; 14, p18−/−; 15, LPA1; 16, Pten−/− Her2/Neu; 17, Stat1−/−; 18, Atx; 19, Lpa2; 20, Lpa3; 21, Twist1 Kras; and 22, Pik3ca-mut p53−/−. See also Supplementary Fig. 1.

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