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Searching for differentially expressed gene combinations

Marcel Dettling1*, Edward Gabrielson12 and Giovanni Parmigiani123

Author Affiliations

1 Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA

2 Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA

3 Department of Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA

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Genome Biology 2005, 6:R88  doi:10.1186/gb-2005-6-10-r88

Published: 19 September 2005

Abstract

We propose 'CorScor', a novel approach for identifying gene pairs with joint differential expression. This is defined as a situation with good phenotype discrimination in the bivariate, but not in the two marginal distributions. CorScor can be used to detect phenotype-related dependencies and interactions among genes. Our easily interpretable approach is scalable to current microarray dimensions and yields promising results on several cancer-gene-expression datasets.