Abstract
Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.
Highlights
From the ‡Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
To demonstrate the features of Graphical Proteomics Data Explorer (GProX), a previously published quantitative proteomics data set comparing phosphoTyrosine dependent signaling 5 and 30 min after epidermal growth factor (EGF) or hepatocyte growth factor (HGF) stimulation [33] was used
To analyze these data sets, the data was imported to GProX specifying the IPI accession keys as protein identifiers and corresponding columns containing the quantitation ratios after EGF or HGF stimulation were allocated to two separate experiments
Summary
As the Bioinformatic Resource Manager [27] and Prequips [28], which both use the program Gaggle [29] for data transfer, provide multifunctional platforms for data analysis. The high expenses associated with these programs and the intransparent nature of commercial software solutions might pose a significant obstacle to the application of these. These issues led us to develop the Graphical Proteomics Data Explorer (GProX), a software package for comprehensive and integrated bioinformatics analysis and visualization of large proteomics data sets. The basic concept of GProX is to provide a data browsing environment similar to common spreadsheet applications and from this interface make available an array of functionalities for analyzing proteomics data. GProX focuses on making available a wide array of useful analysis functions within a single platform and focuses on a user-friendly interface and the production of high-quality graphical objects. The software, as well as the complete source code, is freely available for download from http://gprox.sourceforge.net
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