Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

Abstract

Background: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.Results: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.Conclusions: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks. © 2011 Skinner et al; licensee BioMed Central Ltd.