CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
J Genet Genomics. 2017 May 20;44(5):235-241. doi: 10.1016/j.jgg.2017.05.003. Epub 2017 May 4.
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. Besides, it provides user-friendly web interfaces for querying, browsing and visualizing expression profiles of concerned genes. Together, as a core resource in BIG Data Center, RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
水稻是最重要的稳定粮食作物之一，也是植物研究界的单子叶模式生物。在这里，我们介绍 RED（水稻表达数据库；http://expression.ic4r.org），这是一个完全基于 RNA-Seq 数据的水稻基因表达谱综合数据库。RED 具有 284 个高质量 RNA-Seq 实验的综合数据集，集成了大量的基因表达谱，涵盖了广泛的水稻生长阶段以及各种处理。基于大量的表达谱，RED 提供了一组管家基因和组织特异性基因的列表，并为感兴趣的基因动态构建共表达网络。此外，它还提供了用户友好的 Web 界面，用于查询、浏览和可视化相关基因的表达谱。作为大数据中心的核心资源，RED 对于描述水稻基因的功能以及更好地理解水稻复杂农艺性状背后的重要生物学过程和机制具有重要的应用价值。
