| 引用本文: | 刘伟,魏晓玲,何华勤.VitisMod:一个葡萄基因共表达数据库[J].生物信息学,2023,21(1):60-67. |
| LIU Wei,WEI Xiaoling,HE Huaqin.VitisMod: A database for co-expressed gene modules of grape[J].Chinese Journal of Bioinformatics,2023,21(1):60-67. |
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| 摘要: |
| 葡萄转录组已在各种组织、发育阶段、生物胁迫、非生物胁迫和其他条件下被测定。目前,仍没有简单实用的网络工具来探索这些宝贵的数据。本文从美国国立生物技术信息中心的基因表达数据库(NCBI GEO)下载1019个基因表达芯片数据,进行权重基因共表达网络分析(WGCNA)。鉴定到41个基因共表达模块。功能富集分析发现这些模块具有不同的功能,并与实验/表型相关。通过模块内连接度筛选枢纽基因,这些基因可能具有重要功能。通过关联推定(Guilt-by-association)原理对模块内功能未知的基因进行功能预测。最后,构建了免费的网络工具VitisMod,为葡萄的基因功能研究提供新资源,网址为:http://bioinformatics.fafu.edu.cn/grape。 |
| 关键词: 基因共表达 枢纽基因 连接度 葡萄 网络工具 |
| DOI：10.12113/202106010 |
| 分类号: |
| 文献标识码:A |
| 基金项目:福建农林大学科技创新专项基金项目(No.CXZX2019050G)；福建省自然科学基金项目(No.2019J01381). |
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| VitisMod: A database for co-expressed gene modules of grape |
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LIU Wei, WEI Xiaoling, HE Huaqin
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(College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002,China)
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| Abstract: |
| Grape (Vitis vinifera L.) transcriptomes have been extensively profiled in different tissues, at various developmental stages, under biotic or abiotic stresses, and other conditions. However, there is still no user-friendly tool to explore these precious data. A total of 1 019 microarray sample data were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database (NCBI GEO). Weighted gene correlation network analysis (WGCNA) was conducted. Forty-one gene co-expression modules were identified. Module functional annotation suggested that these modules performed different functions and were associated with experimental conditions/phenotypes. Hub genes, which bear important functions, were screened based on intra-module connectivity. Module genes with unknown functions were annotated according to the “guilt-by-association” rationale. Finally, a web tool VitisMod was developed as a new resource for grape gene function investigation. VitisMod is freely available at http://bioinformatics.fafu.edu.cn/grape/. |
| Key words: Gene co-expression Hub gene Connectivity Vitis vinifera L. Web tool |
