Journal
PROTEOMICS
Volume 12, Issue 3, Pages 406-410Publisher
WILEY
DOI: 10.1002/pmic.201100445
Keywords
Bioinformatics; Functional enrichment; Gene ontology; Normalized spectral abundance factors; Software; Spectral counting
Funding
- Macquarie University
- Australian Research Council
- Australian Government
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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.
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