Fig. 1: Basal breast cancer gene sets are enriched in ESR1 mutant breast cancers.

a Five pairs of luminal/basal gene sets applied in this study with gene numbers specified in each set. b Venn diagram representing the overlap of genes from the basal (left) and luminal (right) gene sets. Genes overlapping in at least four gene sets are indicated. c, d Dot plots showing GSVA score of the five pairs of basal (c) and luminal (d) gene sets enrichment in MCF7 genome-edited cell models. Four biologically independent replicates were used from the original RNA-seq data set (GSE89888) for one time computation. Scores from luminal (n = 33) and basal (n = 39) breast cancer cell lines were used as positive controls. Data are presented as mean ± SD. Dunnett’s test (two-sided) was used to compare with WT-vehicle set within each gene set. e, f Box plots representing basal (e) and luminal (f) gene set enrichments in intra-patient matched paired primary-metastatic samples. Delta GSVA score for each sample was calculated by subtracting the scores of primary tumors from the matched metastatic tumors. Box plots span the upper quartile (upper limit), median (center) and lower quartile (lower limit). Whiskers extend a maximum of 1.5× IQR. Mann–Whitney U-test (two-sided) was performed to compare the Delta GSVA scores between WT (N = 44) or ESR1 mutation-harboring (N = 7) paired tumors. Source data are provided as a Source Data file for c–f.