Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

BACKGROUND: The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO) and the protein-protein interaction network offer alternative views of that structure. RESULTS: This study presents a comparison of the global structures of the Gene Ontology and the interactome of Saccharomyces cerevisiae. Sensitive, unsupervised methods of clustering applied to a large fraction of the proteome led to establish a GO-interactome correlation value of +0.47 for a general dataset that contains both high and low-confidence interactions and +0.58 for a smaller, high-confidence dataset. CONCLUSION: The structures of the yeast cell deduced from GO and interactome are substantially congruent. However, some significant differences were also detected, which may contribute to a better understanding of cell function and also to a refinement of the current ontologies.