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.

基于此研究目标，我们开发了NetREx——基于网络的水稻表达分析服务器（Network-based Rice Expression Analysis Server）。该平台依托统一实验条件下的公开信使RNA（messenger RNA）测序数据，构建并收录了栽培稻（Oryza sativa）的排序共表达网络。平台提供一系列可交互的数据查看器与分析模块，支持用户针对不同胁迫条件（干旱（drought）、淹涝（flood）、低温（cold）与渗透胁迫（osmosis））、激素处理（脱落酸（abscisic acid）与茉莉酸（jasmonic acid））及组织（根（root）与地上部（shoot））中的查询基因开展分析。用户可在预先构建的组织特异性网络中查询自定义基因的子网，进而查看基因的表达倍数变化、模块归属、基因注释信息，并对其邻接基因及相关通路进行分析。