Fig. 1.

Comparison of antisense transcriptomes of normal and neoplastic breast epithelial cells. (A) Percentage of antisense tags relative to all tags in each gene is plotted using average tag counts in all normal (blue) and cancer (red) samples. Orange lines mark 80% and 20% values, which were used as criteria for gene classification into AS, S, and SAS groups. (B) Box plot depicting the percentage of antisense/gene ratio in each normal (blue) and cancer (red) sample. The box indicates the 25th and 75th percentiles; the white bar indicates the median; the whiskers extend to the most extreme data point, which is no more than 1.5 times the interquartile range from the box; and outliers are plotted as small dots. IDC, invasive ductal carcinoma. CD24, CD44, EPCR, and SSEA4 indicate the cell surface markers used for the isolation of epithelial cells (Table S1). (C) Ratio of sense to antisense tag counts in each gene is plotted using average tag counts in all normal (x-axis) and cancer (y-axis) samples. Orange lines mark 4.0 and 0.25 values corresponding to 20% and 80% values of percentage of antisense per gene, respectively. (D) Numbers of AS genes in each sample are shown. Breast cancer cells express a significantly (P = 6.804e-06; Wilcoxon rank-sum test) lower number of AS genes compared with normal samples. (E) Venn diagrams depicting the number of AS genes common among CD24⁺ samples. Significant overlap is observed among samples derived from the same tissue and cell type. Ratios of observed/expected overlaps are 139 and 321 for the CD24.P and CD24.IDC groups, respectively. (F) Scatterplot depicting percentage of antisense tags per gene relative to total tag counts in 252 AS genes common in CD24P cells in normal (blue) and cancer (red) samples. (G) Hierarchical clustering analysis of all samples is based on 252 AS genes common among CD24.P cells. The color scale indicates the percentage of antisense tag counts in each gene.