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Figure 2 | Breast Cancer Research

Figure 2

From: Estrogen receptor negative/progesterone receptor positive breast cancer is not a reproducible subtype

Figure 2

Analyses of estrogen receptor and progesterone receptor mRNA expression in breast cancer. A: Genome-wide analysis of expression variability in ER+ and ER- breast cancer. This smoothed scatterplot shows the distribution of 11,966 genes plotted based on their variability in mRNA levels in ER+ breast cancer (X axis) and ER- breast cancer (Y axis). The color represents the density of genes and ranges from white > beige > gray > black > orange > red, with red the most dense and white the most sparse. We computed the standard deviation (SD) of each gene within ER+ cases (n = 2,505) and ER- cases (n = 1,161). PGR is represented by a red triangle in the bottom-right portion of the plot, demonstrating that PGR shows highly variable expression in ER+ breast cancer (Ranked 157th out of 11,966 genes, 1.3th percentile). Conversely, PGR is one of the least variable genes in ER- breast cancer (Ranked 11,957th out of 11,966 genes, 99.9th percentile). B: Estrogen receptor and progesterone receptor mRNA expression in GEM dataset. This smoothed scatterplot shows the distribution of 4,111 breast tumors. Each tumor is plotted based on its ESR1 expression level (X-Axis) and PGR expression level (Y-Axis). The color represents the data density and ranges from white > beige > gray > black > orange > red, with red the most dense and white the most sparse. The jagged black lines represent the cut-points for converting the continuous mRNA values into a positive/negative binary score. The cut-points used were −1.3 and 0.4 for ESR1 and PGR, respectively. Based on these classification boundaries, 1,316 (32%) of cases were classified as ER+/PR+ (+/+), 1720 (42%) as ER+/PR- (+/−), 1,030 (25%) as ER-/PR- (−/−), and 45 (1%) as ER-/PR+ (−/+).

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