NetREx

With this objective, we have developed NetREx, a Network-based Rice Expression Analysis Server, that hosts ranked co-expression networks of Oryza sativa using publicly available messenger RNA sequencing data across uniform experimental conditions. It provides a range of interactable data viewers and modules for analysing user-queried genes across different stress conditions (drought, flood, cold and osmosis) and hormonal treatments (abscisic and jasmonic acid) and tissues (root and shoot). Subnetworks of user-defined genes can be queried in pre-constructed tissue-specific networks, allowing users to view the fold change, module memberships, gene annotations and analysis of their neighbourhood genes and associated pathways.基于本研究目标，我们开发了NetREx——一款基于网络的水稻表达分析服务器（Network-based Rice Expression Analysis Server）。该服务器依托统一实验条件下公开获取的信使RNA（messenger RNA）测序数据，构建并托管了栽培稻（Oryza sativa）的排名式共表达网络。其提供了一系列交互式数据查看器与分析模块，可针对不同胁迫条件（干旱、洪涝、低温与渗透胁迫）、激素处理（脱落酸（abscisic acid）与茉莉酸（jasmonic acid））及组织（根与地上部）中的用户查询基因开展分析。用户可在预先构建的组织特异性共表达网络中查询自定义基因的子网络，进而查看目标基因的表达倍数变化、模块归属、基因注释信息，以及其邻域基因与相关通路的分析结果。