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aCGH and expression profiling are two major high throughput genomic tools for functional genomics. Although each tool provides invaluable information, full exposition of disease initiation, progression, and manifestation requires synergistic integration of both measurements. In this paper, we will describe an approach to prioritize genomic regions or molecular signatures through the integration of aCGH and expression. Specifically, methods to prioritize genomic regions related to poor survival and related molecular signatures are described. Results obtained by applying our method to a publicly available data set are also presented.