Fig. 2

Basal B cell lines show mesenchymal, stem-like and resistance to treatment characteristics. a–c Gene Set Enrichment Analysis (GSEA) of differentially expressed genes between basal A and B cell lines for three different signatures: Mammary Stem Cell, EMT and Resistance to Gefitinib. Up-regulated genes in all signatures are enriched in basal B cell lines (FDR < 0.25). d Gene ontology analysis bar graphs for differentially expressed (left) and differentially spliced (right) genes between basal A and B cell lines. Gene ontology terms related to Cellular Component (GO_CC_FAT), Molecular Function (GO_MF_FAT) and Biological Process (GO_BP_FAT) are shown in the y axis in blue, yellow and red, respectively. Benjamini false discovery rate (FDR, −log10) is shown on the x-axis. Vertical lines mark an FDR threshold of FDR = 0.05 (−log10(0.05) = 1.3) for differentially expressed and spliced genes, respectively. e. Box plots of the median and 25th percentile of the CD44/CD24 log2 expression ratio for basal A and B cell lines. P value is calculated using the Wilcoxon rank-sum test. f Boxplots comparing IC50 values in basal A and B cell lines upon treatment with different drugs from the Genomics of Drug Sensitivity in Cancer 2 (GDS2) dataset. P values are calculated using the Wilcoxon rank-sum test