PloGO

Plotting gene ontology annotation and abundance in multi-condition proteomics experiments

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

*Corresponding author for this work

Research output: Contribution to journalComment/opinion

24 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)406-410
Number of pages5
JournalProteomics
Volume12
Issue number3
DOIs
Publication statusPublished - Feb 2012

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