Fig. 2

Expression of featured genes in tumors with the ER–/PgR+ phenotype. Box plots of expression of estrogen-responsive genes (a) and basal, claudins, and mesenchymal stem genes (b) for subtypes within ER–/PgR+/HER2– cases from cohort 4. (c) Ratio of TFF1 to EGFR or to CK5 for basal-like (n = 4), luminal-like (n = 11), and other subtypes (n = 2). P values are for comparisons between luminal-like and basal-like by Mann–Whitney test. The probe sets used for gene expression are 205009_at for TFF1, 205862_at for GREB1, 205380_at for PDZK1, 201820_at for KRT5, 205157_s_at for KRT17, 209351_at for KRT14, 201428_at for CLDN4, 202790_at for CLDN7, 203953_s_at for CLDN3, 201130_s_at for CDH1, and 201983_s_at for EGFR. (d) Kaplan–Meier estimates of relapse-free survival according to subgroups within the ER–/PgR+ phenotype using immunohistochemistry-based TFF1 (pS2), KRT5 (CK5), and EGFR. Three groups were defined as follows: luminal-like is defined as TFF1-positive and any CK5 and/or EGFR staining; basal-like is defined as TFF1-negative and positive for at least one marker of CK5 and EGFR; the remaining cases are in the undetermined group. Log-rank P values for pairwise comparison are shown. BL, Basal-like; LL, Luminal-like; NS, Not significant