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.
Department of Biomedical Engineering, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA.
George C
GC
Linderman
Mark R
MR
Chance
Gurkan
G
Bebek
D053263:Gene Regulatory Networks; D020407:Internet; D016015:Logistic Models; D020411:Oligonucleotide Array Sequence Analysis; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics; D012984:Software; D059467:Transcriptome / Q000379:methods*