ArticleBMC plant biology2014
Prediction and functional analysis of the sweet orange protein-protein interaction network.
Article in BMC plant biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 29 citations in OpenAlex.
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- The transcription factors AdNAC3 and AdMYB19 regulate kiwifruit ripening through brassinosteroid and ethylene signaling networks.Plant physiology · 2025Article
- Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet.International journal of molecular sciences · 2022Article
- Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow.Life (Basel, Switzerland) · 2022Review
- CPIELA: Computational Prediction of Plant Protein-Protein Interactions by Ensemble Learning Approach From Protein Sequences and Evolutionary Information.Frontiers in genetics · 2022Article
- Molecular Analysis ofInternational journal of molecular sciences · 2021Article
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- PlaPPISite: a comprehensive resource for plant protein-protein interaction sites.BMC plant biology · 2020Article
- A predicted protein functional network aids in novel gene mining for characteristic secondary metabolites in tea plantJournal of biosciences · 2020Article
- Genome-wide identification, characterization, interaction network and expression profile ofPeerJ · 2019Article
- Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.Proteomes · 2018Article
- Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize.Frontiers in chemistry · 2018Article
- Prediction of cassava protein interactome based on interolog method.Scientific reports · 2017Article
- Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2017Article
- Prediction of Protein-Protein Interactions by Evidence Combining Methods.International journal of molecular sciences · 2016Review
- Construction of citrus gene coexpression networks from microarray data using random matrix theory.Horticulture research · 2015Article
- A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.Frontiers in genetics · 2015Article
- Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species.
resultsIn this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks.
conclusionsGene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.
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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.