The Gene Ontology − Providing a Functional Role in Proteomic Studies

Until recently, biologists have concentrated on studying specifi c pathways or individual molecules as an approach to unravelling the intricate details of cellular events. However recent advances in high-throughput proteomic methodologies have made it possible to profi le the global compositions of entire tissues, organelles or interactomes at specifi c time points or under particular developmental or disease states. While such methods provide researchers with a greater understanding of large-scale, complex biological changes, it has necessitated an increasing reliance on standardised annotation to link results to known biological activities. The Gene Ontology (GO) Consortium provides standardised functional annotations, which support high-throughput analyses and systems biology by enabling genes or proteins to be classifi ed and grouped according to their function, involvement in a particular process or subcellular location, providing researchers with an indication of underlying mechanisms behind a certain phenotype. In this article we provide an overview of the Gene Ontology, its uses and the software available for the analysis of proteomic data. Many of the examples presented in this paper relate to cardiovascular studies, the focus of a new GO annotation initiative. Abbreviations: GO, Gene Ontology GOC, Gene Ontology Consortium GOA, Gene Ontology Annotation database