ArticleJournal, genetic engineering & biotechnology2023
Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa).
Article in Journal, genetic engineering & biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 36 citations in OpenAlex.
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- Comparative transcriptomic analysis identifies conserved abiotic stress-responsive hub genes in Sorghum bicolor.BMC plant biology · 2026Article
- Network Clustering Approach Reveals Key Proteins and Biological Functions in the Response of Whiteleg Shrimp (Penaeus vannamei) to Acute Hepatopancreatic Necrosis Disease.Marine biotechnology (New York, N.Y.) · 2026Article
- Pangenome-wide identification of chloroplast RNA splicing and ribosome maturation (CRM) genes in eight Pyrus genomes indicated their involvement in multiple stresses.Scientific reports · 2026Article
- Evaluating network-based algorithms for protein function prediction using plant protein-protein interaction networks.BMC plant biology · 2026Article
- Article
- Identification of Ageing-related Hub Genes in Humans, Mouse and Rat Based on Bioinformatics Analysis.Annals of neurosciences · 2025Article
- Recent Advances and Application of Machine Learning for Protein-Protein Interaction Prediction in Rice: Challenges and Future Perspectives.Proteomes · 2025Review
- Prediction of new candidate proteins and analysis of sub-modules and protein hubs associated with seed development in rice (Oryza sativa) using an ensemble network-based systems biology approach.BMC plant biology · 2025Article
- Genome-Wide Analysis of theInternational journal of molecular sciences · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Transcriptomic and protein-protein interaction network analyses of the molecular mechanisms underlying the mycorrhizal interaction inFrontiers in plant science · 2025Article
- Targeting Tumor Differentiation Grade-related Genes Prognostic Signature Including COL5A1 Based on Single-cell RNA-seq in Gastric Cancer.International journal of medical sciences · 2025Article
- CDK4 as a Prognostic Marker of Hepatocellular Carcinoma and CDK4 Inhibitors as Potential Therapeutics.Current medicinal chemistry · 2025Article
- Genetic dissection of root traits in a rice 'global MAGIC' population for candidate traits to breed for reduced methane emission.Frontiers in plant science · 2025Article
- Biomedical literature mining: graph kernel-based learning for gene-gene interaction extraction.European journal of medical research · 2024Article
- Antiproliferative Activity of Piceamycin by RegulatingBiomolecules & therapeutics · 2024Article
- Protein-protein interaction network module changes associated with the vertebrate fin-to-limb transition.Scientific reports · 2023Article
- Network interactions with functional roles and evolutionary relationships for BURP domain-containing proteins in chickpea and model species.Bioinformation · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance.
resultsHere, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs.
conclusionsThese results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.
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