Author ORCID Identifier
Document Type
Article
Publication Date
6-4-2012
Abstract
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.
Publication Title
Nucleic Acids Research
Grant
P30CA043703
Rights
© The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Recommended Citation
George C. Linderman, Mark R. Chance, Gurkan Bebek, MAGNET: MicroArray Gene expression and Network Evaluation Toolkit, Nucleic Acids Research, Volume 40, Issue W1, 1 July 2012, Pages W152–W156, https://doi.org/10.1093/nar/gks526
Manuscript Version
Final Publisher Version