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PloGO: Plotting gene ontology annotation and abundance in multi‐condition proteomics experiments
Author(s) -
Pascovici Dana,
Keighley Tim,
Mirzaei Mehdi,
Haynes Paul A.,
Cooke Brett
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100445
Subject(s) - proteomics , gene ontology , annotation , ontology , computational biology , abundance (ecology) , computer science , biology , bioinformatics , gene , genetics , gene expression , ecology , philosophy , epistemology
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.