ArticleRice (New York, N.Y.)2012
A predicted protein interactome for rice.
Article in Rice (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses.BioMed research international · 2019Pooled it
- Global Protein Interactome Mapping in Rice Using Barcode-Indexed PCR Coupled with HiFi Long-Read Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structure-based prediction of protein-protein interaction network in rice.Genetics and molecular biology · 2024Article
- An interolog-based barley interactome as an integration framework for immune signaling.Genetics · 2022Article
- Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management.Frontiers in plant science · 2021Review
- Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes.International journal of molecular sciences · 2020Article
- Exploring dynamic protein-protein interactions in cassava through the integrative interactome network.Scientific reports · 2020Article
- Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing withInternational journal of molecular sciences · 2019Article
- Infrastructures of systems biology that facilitate functional genomic study in rice.Rice (New York, N.Y.) · 2019Review
- Genome-wide analysis of root hair-preferential genes in rice.Rice (New York, N.Y.) · 2018Article
- The Interactomic Analysis Reveals Pathogenic Protein Networks inFrontiers in genetics · 2018Article
- Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles.Plant molecular biology · 2018Article
- Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs.Frontiers in plant science · 2018Review
- Prediction of cassava protein interactome based on interolog method.Scientific reports · 2017Article
- Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons.BMC genomics · 2017Article
- OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.Frontiers in plant science · 2017Article
- Techniques for the Analysis of Protein-Protein Interactions in Vivo.Plant physiology · 2016Review
- A Network Approach of Gene Co-expression in theFrontiers in genetics · 2016Article
- Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.Plant physiology · 2015Article
- Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein-protein interactions (PPIs) create the steps in signaling and regulatory networks central to most fundamental biological processes. It is possible to predict these interactions by making use of experimentally determined orthologous interactions in other species.
resultsIn this study, prediction of PPIs in rice was carried out by the interolog method of mapping deduced orthologous genes to protein interactions supported by experimental evidence from reference organisms. We predicted 37112 interactions for 4567 rice proteins, including 1671 predicted self interactions (homo-interactions) and 35441 predicted interactions between different proteins (hetero-interactions). These matched 168 of 675 experimentally-determined interactions in rice. Interacting proteins were significantly more co-expressed than expected by chance, which is typical of experimentally-determined interactomes. The rice interacting proteins were divided topologically into 981 free ends (proteins with single interactions), 499 pipes (proteins with two interactions) and 3087 hubs of different sizes ranging from three to more than 100 interactions.
conclusionsThis predicted rice interactome extends known pathways and improves functional annotation of unknown rice proteins and networks in rice, and is easily explored with software tools presented here.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.