James R. Ortega
Compound efficacy, compound specificity, and target identification are crucial for successful cancer therapeutics. The accurate characterization of genetic determinants of compound sensitivity in cancer cells would advance drug discovery, particularly in patients with known genetic lesions, and ultimately improve outcomes for patients. We characterized NCI-60 cancer cell line compound-sensitivity profiles with respect to gene-expression measurements. We used a novel analysis method that combines a Spearman rank-correlation algorithm for feature selection with elastic net regression analysis for predictive model generation. Using this approach, we identified several candidate gene lists (weighted by importance) that appear to predict sensitivity. Using biological pathway analysis, we studied the underlying biological networks relevant to compound sensitivity and cancer. These biological networks suggest several targets for anti-cancer compound development, and provide a framework for continued analysis of the connection between compound efficacy/specificity analyses and genetic characterization of cancer cells.
PROJECT: Development of Predictive Models to Identify Pathways Relevant to Compound Sensitivity in Cancer
Mentors: Paul Clemons & Amrita Basu, Chemical Biology Program
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