DNA microarray based gene expression analysis of primary breast cancers is not in general clinical use in spite of the widespread enthusiasm for the approach. However, several studies have identified gene expression patterns, or "signatures" that are predictive of disease outcome and assays based on these findings have become commercially available. Additional studies are required to further define gene signatures that can be used to help tailor the therapy best suited to for an individual patient. Recent gene expression profiling studies using cell line models to identify downstream transcriptional targets of oncogenic signaling pathways may help achieve this goal.