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论文题目: Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm
英文论文题目: Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm
第一作者: Zhang, YH; Dai, L; Liu, Y; Zhang, YH; Wang, SP
英文第一作者: Zhang, YH; Dai, L; Liu, Y; Zhang, YH; Wang, SP
联系作者: Zhang, YH (reprint author), Anhui Agr Univ, Sch Resources & Environm, Hefei, Peoples R China.
英文联系作者: Zhang, YH (reprint author), Anhui Agr Univ, Sch Resources & Environm, Hefei, Peoples R China.
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发表年度: 2017
卷: 12
期: 5
页码: e0177017
摘要: Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.
英文摘要: Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.
刊物名称: PLOS ONE
英文刊物名称: PLOS ONE
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学科: Multidisciplinary Sciences
英文学科: Multidisciplinary Sciences
影响因子: 2.806
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论文类别: Article
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