GOEx :: Gene Ontology Explorer

Here we present a new algorithm, termed GO Explorer (GOEx), that leverages the gene ontology (GO) to aid in the interpretation of proteomic data.  GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions.  Moreover, it is bult within PatternLab for Proteomics project, a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting.  GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. All in all, GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface.  It is a useful, friendly, and simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics.

For further details, please verify our manuscript by clicking below:

GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomics, Proteome Science 2009, 7:6

* A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alterantive strategy, there will be no protein fold information.