Comparisons of Predicted Genetic Modules: Identification of Co-Expressed Genes through Module Gene Flow

Boris E Shakhnovich (borya@bu.edu)
Timothy E Reddy (treddy@bu.edu)
Kevin Galinsky (galinsky@bu.edu)
Joseph Mellor (mellor@bu.edu)
Charles Delisi (delisi@bu.edu)

Boston University Bioinformatics Program, Boston University, Boston, MA 02215, USA


Abstract

A question of fundamental importance is the definition and identification of modules from microarray experiments. A wide variety of techniques have been used to gain insight into the elucidation of such modules. One problem, however, is the inability to directly compare results between the different data sets produced due to the inherent parameterizations of their approaches. We first aim to provide a mechanism by which different approaches to module finding can be directly compared. Moreover, the same approach can be used to internally compare the modules predicted by the same technique, but at different parameterizations. We apply this approach to analyze the flow of genes through modules at different module thresholds of the Barkai Signature method, thereby further resolving the modules into sets of co-expressed genes.

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Japanese Society for Bioinformatics