title: Filtering and interpreting large-scale experimental protein-protein interaction data.
abstract: Rarely acting in isolation, it is invariably the physical associations among proteins that define their biological activity, necessitating the study of the cellular meshwork of protein-protein interactions (PPI) before a full appreciation of gene function can be achieved. The past few years have seen a marked expansion in the both the sheer volume and number of organisms for which high-quality interaction data is available, with high-throughput interaction screening and detection techniques showing consistent improvement both in scale and sensitivity. Although techniques for large-scale PPI mapping are increasingly being applied to new organisms, including human, there is a corresponding need to rigorously evaluate, benchmark, and impartially filter the results. This chapter explores methods for PPI dataset evaluation, including a survey of previous techniques applied by landmark studies in the field and a discussion of promising new experimental approaches. We further outline practical suggestions and useful tools for interpreting newly generated PPI data. As the majority of large-scale experimental data has been generated for the budding yeast S. cerevisiae, most of the techniques and datasets described are from the perspective of this model unicellular eukaryote; however, extensions to other organisms including mammals are mentioned where possible.
authors.affiliation: Cardiovascular Division, Brigham & Women's Hospital, Boston, MA, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Musso
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.forename: Zhaolei
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D030562:Databases, Protein; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins