Breast cancer is a heterogeneous disease and existing
clinicopathological classifications do not fully capture the
diversity in clinical disease course. Since the oestrogen
receptor (ER) plays a central role in the crosstalk between different signalling pathways in breast cancer, the expression of this receptor is important for the behaviour of breast cancer cells and is reflected in gene expression patterns of breast tumours. High throughput analysis of gene expression of breast cancer has increased the insights into ER signalling, including its relation with disease outcome and therapy response. Expression of ER and its numerous downstream targets are driving patterns of gene expression and dominate unsupervised analyses in the breast cancer specimens studied to date, regardless of microarray platform or statistical approach. This paper reviews gene expression studies either attempting to unravel the functional effect of ER or describing the gene expression profiles driven by ER in breast tumours. In addition, the development of molecular signatures predicting response to endocrine treatment will be discussed.