NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data

EA McClellan, PD Moerland, Peter van der Spek, Andrew Stubbs

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Abstract

The discovery of functionally related groups in a set of significantly abundant proteins from a mass spectrometry experiment is an important step in a proteomics analysis pipeline. Here we describe NetWeAvers (Network Weighted Averages) for analyzing groups of regulated proteins in a network context, e. g. as defined by clusters of protein-protein interactions. NetWeAvers is an R package that provides a novel method for analyzing proteomics data integrated with biological networks. The method includes an algorithm for finding dense clusters of proteins and a permutation algorithm to calculate cluster P-values. Optional steps include summarizing quantified peptide values to single protein values and testing for differential expression, such that the data input can simply be a list of identified and quantified peaks.
Original languageUndefined/Unknown
Pages (from-to)2946-2947
Number of pages2
JournalBioinformatics
Volume29
Issue number22
DOIs
Publication statusPublished - 2013

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