Introduction

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION:  The NetWeAvers package is written in R, is open source and is freely available on CRAN and from netweavers.erasmusmc.nl under the GPL-v2 license. CONTACT: e.mcclellan@erasmusmc.nl

Publications

  1. NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data.
    Cite this
    McClellan EA, Moerland PD, van der Spek PJ, Stubbs AP, 2013-11-01 - Bioinformatics (Oxford, England)

Credits

  1. Elizabeth A McClellan
    Developer

    Department of Bioinformatics, Erasmus University Medical Center

  2. Perry D Moerland
    Developer

  3. Peter J van der Spek
    Developer

  4. Andrew P Stubbs
    Investigator

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Summary
AccessionBT000190
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew P Stubbs