Detection of functional modules from protein interaction networks

Complex cellular processes are modular and are accomplished by the concerted action of functional modules (Ravasz et al., Science 2002;297:1551–1555; Hartwell et al., Nature 1999;402:C47–52). These modules encompass groups of genes or proteins involved in common elementary biological functions. One important and largely unsolved goal of functional genomics is the identification of functional modules from genomewide information, such as transcription profiles or protein interactions. To cope with the ever‐increasing volume and complexity of protein interaction data (Bader et al., Nucleic Acids Res 2001;29:242–245; Xenarios et al., Nucleic Acids Res 2002;30:303–305), new automated approaches for pattern discovery in these densely connected interaction networks are required (Ravasz et al., Science 2002;297:1551–1555; Bader and Hogue, Nat Biotechnol 2002;20:991–997; Snel et al., Proc Natl Acad Sci USA 2002;99:5890–5895). In this study, we successfully isolate 1046 functional modules from the known protein interaction network of Saccharomyces cerevisiae involving 8046 individual pair‐wise interactions by using an entirely automated and unsupervised graph clustering algorithm. This systems biology approach is able to detect many well‐known protein complexes or biological processes, without reference to any additional information. We use an extensive statistical validation procedure to establish the biological significance of the detected modules and explore this complex, hierarchical network of modular interactions from which pathways can be inferred. Proteins 2003. © 2003 Wiley‐Liss, Inc.