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MetaNetwork: Enhancing biological interpretation of proteomics data with weighted gene correlation network analysis (WGCNA)

MetaNetwork is a free, open-source, R-based application that performs weighted gene correlation network analysis on proteomics data (WGCNA). WGCNA creates networks of proteins that are correlated across samples and uses unsupervised clustering to group proteins into "modules." Each module contains groups of proteins that represent biological pathway. These pathways can be identified using MetaNetwork's gene ontology enrichment analysis.

Getting started

The README page details how to install and start MetaNetwork.

This wiki provides two vignettes for understanding how to use both the WGCNA and functional annotation features of MetaNetwork to analyze a proteomics experiment. The vignette summarizes the output of MetaNetwork and how to use eigenprotein analysis to interpret proteomics data.