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The use of advanced 'omics' technologies, especially in specific gene expression profiling, has increased gradually in recent years. In basic research, high throughput profiling applications are increasingly used and may now even be considered standard research tools. In the clinic, there is an urgent need for specific diagnosis, prognosis and treatment response indicators. For theses reasons, clinicians have looked to the new field of omics technologies as a new aspect for biomarkers discovery. These prediction tools have attracted the attention of basic researchers needs to discover biological mechanisms underlying clinically useful signal pathways. In the present chapter we will highlight some of the seminal work establishing the arrival of the omics particularly in breast cancer research and will discuss a sample of the most current applications. We will in addition discuss the challenges of data analysis and integrated data analysis with emphasis on the use of the current publicly available gene expression datasets.