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Open Access Research article

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

Antonio Marco1 and Ignacio Marín2*

Author Affiliations

1 Center for Evolutionary Functional Genomics, The Biodesign Institute, Tempe, Arizona State University, USA

2 Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain

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BMC Systems Biology 2009, 3:69  doi:10.1186/1752-0509-3-69

Published: 15 July 2009

Abstract

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.