title: Prediction and functional analysis of the sweet orange protein-protein interaction network.
abstract: BACKGROUND
  Sweet 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Gene 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.
authors.forename: Yu-Duan
authors.initials: YD
authors.lastname: Ding
authors.forename: Ji-Wei
authors.initials: JW
authors.lastname: Chang
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.forename: Dijun
authors.initials: D
authors.lastname: Chen
authors.forename: Sen
authors.initials: S
authors.lastname: Li
authors.forename: Qiang
authors.initials: Q
authors.lastname: Xu
authors.forename: Xiu-Xin
authors.initials: XX
authors.lastname: Deng
authors.affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. yjcheng@mail.hzau.edu.cn.
authors.forename: Yun-Jiang
authors.initials: YJ
authors.lastname: Cheng
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D032084:Citrus sinensis / Q000235:genetics / Q000378:metabolism*; D018745:Genome, Plant; D010937:Plant Growth Regulators / Q000378:metabolism; D060066:Protein Interaction Maps; D017423:Sequence Analysis, RNA
chemical_list: D010937:Plant Growth Regulators
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