title: Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling.
abstract: Protein-protein interactions (PPIs) are essential to almost all cellular processes. To better understand the relationships of proteins in Arabidopsis (Arabidopsis thaliana), we have developed a genome-wide protein interaction network (AraPPINet) that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins. AraPPINet exhibited high predictive power for discovering protein interactions at a 50% true positive rate and for discriminating positive interactions from similar protein pairs at a 70% true positive rate. Experimental evaluation of a set of predicted PPIs demonstrated the ability of AraPPINet to identify novel protein interactions involved in a specific process at an approximately 100-fold greater accuracy than random protein-protein pairs in a test case of abscisic acid (ABA) signaling. Genetic analysis of an experimentally validated, predicted interaction between ARR1 and PYL1 uncovered cross talk between ABA and cytokinin signaling in the control of root growth. Therefore, we demonstrate the power of AraPPINet (http://netbio.sjtu.edu.cn/arappinet/) as a resource for discovering gene function in converging signaling pathways and complex traits in plants.
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Fangyuan
authors.identifier: 0000-0002-9309-9577
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Shiwei
authors.identifier: 0000-0003-4711-5959
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Ling
authors.identifier: 0000-0001-5194-0391
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Kaijing
authors.initials: K
authors.lastname: Zuo
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Lingxia
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China zhangld@sjtu.edu.cn.
authors.forename: Lida
authors.identifier: 0000-0002-5207-2458
authors.initials: L
authors.lastname: Zhang
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D017360:Arabidopsis / Q000378:metabolism; D003583:Cytokinins / Q000378:metabolism; D005453:Fluorescence; D018745:Genome, Plant; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D018517:Plant Roots / Q000254:growth & development / Q000378:metabolism; D060066:Protein Interaction Maps; D015203:Reproducibility of Results; D036226:Seedlings / Q000378:metabolism; D015398:Signal Transduction; D020798:Two-Hybrid System Techniques
chemical_list: D003583:Cytokinins; D000040:Abscisic Acid