Abstract: This invention is a model that simulates the complexity of biological signaling in a cell in response to radiation therapy. Using gene expression profiles and radiation survival assays in an algorithm, a systems model was generated of the radiosensitivity network. The network consists of ten highly interconnected genetic hubs with significant signal redundancy. The model was validated with in vitro tests perturbing network components, correctly predicting radiation sensitivity 2/3 times. The model's clinical relevance was shown by linking clinical radiosensitivity targets to the model network. Clinical applications were confirmed by testing model predictions against clinical response to preoperative radiochemotherapy in patients with rectal or esophageal cancer.

Abstract: The invention provides a molecular marker set that can be used for prognosis of colorectal cancer in a colorectal cancer patient. The invention also provides methods and computer systems for evaluating prognosis of colorectal cancer in a colorectal cancer patient based on the molecular marker set. The invention also provides methods and computer systems for determining chemotherapy for a colorectal cancer patient and for enrolling patients in clinical trials.

Abstract: A classifier to predict cellular radiation sensitivity based on gene expression profiles in thirty-five cell lines from the NCI panel of 60 cancer cell lines (NCI-60), using a novel approach to predictive gene analysis. Three novel genes are provided, retinoblastoma binding protein 4 (RbAp48), G-protein signaling regulator 19 (RGS19) and ribose-5-phosphate isomerase A (R5PIA) whose expression values were correlated with radiation sensitivity.