Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm
文献类型：期刊论文
| 作者 | Zhang, Yunhua3; Dai, Li3; Liu, Ying2; Zhang, YuHang4; Wang, ShaoPeng1; , |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2017 |
| 卷号 | 12期号:5页码:e0177017 |
| 关键词 | Multivariate analysis Structured kernel principal component regression Association study Functional connectivity |
| ISSN号 | 1932-6203 |
| DOI | 10.1371/journal.pone.0177017 |
| 文献子类 | Article |
| 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. |
| 学科主题 | Science & Technology - Other Topics |
| WOS关键词 | PROTEIN-PROTEIN INTERACTIONS ; ONE-CARBON METABOLISM ; SEED-GERMINATION ; SHORTEST-PATH ; SPECIFICALLY INTERACTS ; COMPUTATIONAL METHOD ; IDENTIFICATION ; NETWORK ; PREDICTION ; PLANTS |
| 语种 | 英语 |
| WOS记录号 | WOS:000400648500118 |
| 出版者 | PUBLIC LIBRARY SCIENCE |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1146]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Shanghai Univ, Sch Life Sci, Shanghai, Peoples R China, 2.Anhui Agr Univ, Sch Forestry & Landscape Architecture, Hefei, Peoples R China; 3.Anhui Agr Univ, Sch Resources & Environm, Hefei, Peoples R China; 4.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Zhang, Yunhua,Dai, Li,Liu, Ying,et al. Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm[J]. PLOS ONE,2017,12(5):e0177017. |
| APA | Zhang, Yunhua,Dai, Li,Liu, Ying,Zhang, YuHang,Wang, ShaoPeng,&,.(2017).Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm.PLOS ONE,12(5),e0177017. |
| MLA | Zhang, Yunhua,et al."Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm".PLOS ONE 12.5(2017):e0177017. |
入库方式： OAI收割
来源：上海营养与健康研究所
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