Interactome: gateway into systems biologyMichael E. Cusick1,*, Niels Klitgord1, Marc Vidal1,2and David E. Hill1,21Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 BinneyStreet, Boston, MA 02115, USA and2Department of Genetics, Harvard Medical School, Boston, MA 02115, USAReceived August 18, 2005; Revised and Accepted September 1, 2005Protein–protein interactions are fundamental to all biological processes, and a comprehensive determinationof all protein –protein interactions that can take place in an organism provides a framework for understandingbiol ogy as an integrated system. The availabi lity of genome-scale sets of cloned open reading fr ames hasfacilitate d systematic efforts at creating proteome-s cale data sets of prot ein – protein interactions , whichare represented as complex networks or ‘interactome’ maps. Protein – protein interaction mapping projectsthat follow stringent cr iteria, coupled with experimenta l validation in orthogonal systems, provide high-confidence data sets immanently useful for interrogating developmental and disease mechanisms at asystem level as well as elucidating indiv idual protei n function and interactome network top ology. Althoughfar from complete, currently available maps provide insight into how biochemical properties of proteins andprotein compl exes are i ntegra ted i nto biological systems. Such maps are also a useful resource to pr edictthe fun ction(s) of thousands of genes.SYSTEMATIC MAPPING OF INTERACTOMENETWORKSMost gene products mediate their function within complex net-works of interconnected macromolecules. Studies in modelorganisms suggest that complex macromolecular networkshave topological and dynamic properties that reflect biol ogicalphenomena (1,2). Thus, an understanding of biological mech-anisms and disease processes demands a ‘systems’ approachthat goes beyond one-at-a-time studies of single componentsto more global analyses of the structure, function and dynamicsof the networks in which macromolecules function.We consider the full interactome network as the completecollection of all physical protein –protein interactions that cantake place within a cell. Construction of comprehensive setsof protein –protein interactions, interactomes , requires the cre-ation of genome-scale resource collections of open readingframes (ORFeomes) cloned so as to facilitate proteinexpression, generated iteratively based on improved genepredictions and experimental verification and capturing allexpressed isoforms (splice variants and polymorphisms).ORFeomes, as faithful representations of the encodedproteome, provide the starting material for carrying out high-throughput interaction studies that are then validated by orthog-onal interaction methods. The resulting interactome maps areregarded as ‘framework’ information; and by integratingother functional genomic and proteomic data sets, increasinglydetailed and reliable biological models can be generated (3).Model organisms have provided the basis for a systematiccharacterization of physical protein–protein interactions(‘interactome’ mapping). Initial efforts focused on definedbiological processes or ‘modules’ for the yeast Saccharomycescerevisiae and the worm Caenorhabditis elegans (4,5).Subsequently, proteome-scale interactome mapping projectsfor eukaryotes have been carried out in yeast, worm and fly(6–10). Current estimates for the complete yeast interactomesuggest ! 28 000 potential protein interactions, on the basisof experimental and computational analyses (6,7,11 – 15)along with incorporating literature-curated interactions suchas those collected in the MIPS databases (16). So far, theworm and fly interactome maps each contain approximately5000 high-quality putative interactions derived primarilyfrom high-throughput yeast two-hybrid (Y2H) screens(8–10). These two data sets demonstrate the feasibility ofinteractome mapping projects for metazoans, and they alsoillustrate the power of integrating multiple approaches tomodel biological networks (17). However, to fully understandhuman biology and the molecular mechanisms underlying dis-eases such as cancer, systematic experimental mapping of thehuman interactome itself is necessary.Although completed genome sequences provide lists of tensof thousands of predicted unique proteins (! 25 000 for the# The Author 2005. Published by Oxford University Press. All rights reserved.For Permissions, please email: [email protected]*To whom correspondence should be addressed. Tel: þ1 6176323802; Fax: þ1 6176325739; Email: [email protected];[email protected]; [email protected] Molecular Genetics, 2005, Vol. 14, Review Issue 2 R171–R181doi:10.1093/hmg/ddi335human proteome, disregarding splice variants and post-translational modifications), the sequences by themselves donot provide an understanding of the underlying principles ofcellular systems. Proteome-s cale information is also requiredat structural, functional and dynamic levels. This informationshould encompass various molecular networks, such as regu-latory, biochemical or protein–protein interaction networks.The initial challenge is the generation of comprehensivenetwork maps, generally depicted as nodes (e.g. proteins,RNAs, DNA binding sites or metabolites) linked by edgescorresponding to molecular interactions (e.g. protein–proteininteractions, enzymatic reactions, DNA– protein, etc.).For each network map, individual nodes and edges need tobe perturbed systematically to help in understanding thelogic of molecular networks involved in any biologicalprocesses of interest. As biological systems are highlydynamic and fluid, information on where and when nodesappear or disappear on where and when edges take placeand on the rewiring of the network, as sub-networks appearor disappear during developmental and cell cycle stages,needs to be obtained.Here, we review recent progress in interactome mapping,emphasizing the need for high-confidence, experimentallyderived data sets to drive the construction and use of thesemaps as frameworks for integrating other genome-scale infor-mation, such as genetic interactions, expression profiling andphenotypic analyses.FUNCTIONALITY AND MULTIFUNCTIONALITYA significant hindrance to a comprehensive understanding ofhuman biology, encompassing both the individual parts andthe integrated whole, is the