Proteomics. 2012 Feb;12(3):406-10. doi: 10.1002/pmic.201100445. Epub 2012 Jan 18.

PloGO: plotting gene ontology annotation and abundance in multi-condition proteomics experiments.

Proteomics

Dana Pascovici, Tim Keighley, Mehdi Mirzaei, Paul A Haynes, Brett Cooke

PMID: 22213732 DOI: 10.1002/pmic.201100445

Abstract

We describe the PloGO R package, a simple open-source tool for plotting gene ontology (GO) annotation and abundance information, which was developed to aid with the bioinformatics analysis of multi-condition label-free proteomics experiments using quantitation based on spectral counting. PloGO can incorporate abundance (raw spectral counts) or normalized spectral abundance factors (NSAF) data in addition to the GO annotation, as well as handle multiple files and allow for a targeted collection of GO categories of interest. Our main aims were to help identify interesting subsets of proteins for further analysis such as those arising from a protein data set partition based on the presence and absence or multiple pair-wise comparisons, as well as provide GO summaries that can be easily used in subsequent analyses. Though developed with label-free proteomics experiments in mind it is not specific to that approach and can be used for any multi-condition experiment for which GO information has been generated.

Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MeSH terms

• Computational Biology / methods
• Databases, Protein
• Humans
• Molecular Sequence Annotation*
• Proteomics / methods
• Software*

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't