ArticlePlant physiology2016
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species.GigaScience · 2025Article
- Homologous mapping yielded a comprehensive predicted protein-protein interaction network for peanut (Arachis hypogaea L.).BMC plant biology · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Structure-based prediction of protein-protein interaction network in rice.Genetics and molecular biology · 2024Article
- Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein-protein interactions.Plant methods · 2023Article
- CALMODULIN-LIKE-38 and PEP1 RECEPTOR 2 integrate nitrate and brassinosteroid signals to regulate root growth.Plant physiology · 2021Article
- Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network.Scientific reports · 2021Article
- Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches.Frontiers in plant science · 2021Article
- Ribosomal Protein RPL10A Contributes to Early Plant Development and Abscisic Acid-Dependent Responses inFrontiers in plant science · 2020Article
- Chemodiversity of the Glucosinolate-Myrosinase System at the Single Cell Type Resolution.Frontiers in plant science · 2019Review
- AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk inFrontiers in plant science · 2019Article
- Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.Proteomes · 2018Article
- BPH1, a novel substrate receptor of CRL3, plays a repressive role in ABA signal transduction.Plant molecular biology · 2018Article
- Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs.Frontiers in plant science · 2018Review
- Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana.Genetics and molecular biologyArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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