title: Fundamentals of protein interaction network mapping.
abstract: Studying protein interaction networks of all proteins in an organism ("interactomes") remains one of the major challenges in modern biomedicine. Such information is crucial to understanding cellular pathways and developing effective therapies for the treatment of human diseases. Over the past two decades, diverse biochemical, genetic, and cell biological methods have been developed to map interactomes. In this review, we highlight basic principles of interactome mapping. Specifically, we discuss the strengths and weaknesses of individual assays, how to select a method appropriate for the problem being studied, and provide general guidelines for carrying out the necessary follow-up analyses. In addition, we discuss computational methods to predict, map, and visualize interactomes, and provide a summary of some of the most important interactome resources. We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research.
authors.affiliation: Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
authors.forename: Jamie
authors.initials: J
authors.lastname: Snider
authors.affiliation: Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada.
authors.forename: Max
authors.initials: M
authors.lastname: Kotlyar
authors.affiliation: Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
authors.forename: Punit
authors.initials: P
authors.lastname: Saraon
authors.affiliation: Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Princess Margaret Cancer Center, IBM Life Sciences Discovery Centre, University Health Network, Ontario, Canada.
authors.forename: Igor
authors.initials: I
authors.lastname: Jurisica
authors.affiliation: Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada igor.stagljar@utoronto.ca.
authors.forename: Igor
authors.initials: I
authors.lastname: Stagljar
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D006801:Humans; D008322:Mammals / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: PPI technologies; bioinformatics; interactome mapping; protein‐protein interactions (PPIs); proteomics