Abstract: Disclosed herein are methods for detecting and identifying potential breast cancer biomarkers in an individual patient. Also disclosed are newly discovered breast cancer markers set forth in Tables I, II and III, associated with the cancerous state of breast cells. It has been discovered that a higher than normal level of expression of any of these markers or combination of these markers correlates with breast cancer in a patient. Methods are provided for detecting the presence of breast cancer in a sample, the absence of breast cancer in a sample, the stage of breast cancer, assessing whether a breast cancer has metastasized, predicting the likely clinical outcome of a breast cancer patient, and with other characteristics of breast cancer that are relevant to prevention, diagnosis, characterization, and therapy of breast cancer in a patient.