MAGNET: MicroArray Gene expression and Network Evaluation Toolkit

MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein–protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weighted gene–gene and protein–protein interaction networks. MAGNET allows users to weight edges of protein–protein interaction networks using a logistic regression model integrating tissue-specific gene expression data, sub-cellular localization data, co-clustering of interacting proteins and the number of observations of the interaction. This provides a way to quantitatively measure the plausibility of interactions in protein–protein interaction networks given protein/gene expression measurements. Secondly, MAGNET generates filtered coexpression networks, where genes are represented as nodes, and their correlations are represented with edges. Overall, MAGNET provides researchers with a new framework with which to analyze and generate gene–gene and protein–protein interaction networks, based on both the user’s own data and publicly available –omics datasets. The freely available service and documentation can be accessed at http://gurkan.case.edu/software or http://magnet.case.edu.