School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
Planta. 2019 May;249(5):1487-1501. doi: 10.1007/s00425-019-03102-9. Epub 2019 Jan 30.
A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These data can be reused for research on gene function through a systematic analysis of gene co-expression relationships. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus, identified modules of co-expressed genes and annotated module functions. These modules were associated with experiments/traits, which provided potential signature modules for phenotypes. Novel heat shock proteins were implicated according to guilt by association. A higher-order module networks analysis suggested that the Arabidopsis network can be further organized into 15 meta-modules and that a chloroplast meta-module has a distinct gene expression pattern from the other 14 meta-modules. A comparison with the rice transcriptome revealed preserved modules and KEGG pathways. All the module gene information was available from an online tool at http://bioinformatics.fafu.edu.cn/arabi/ . Our findings provide a new source for future gene discovery in Arabidopsis.
对拟南芥转录组进行了全面的网络分析，该分析可能成为候选基因功能研究的有价值资源。还提供了一个用于探索模块信息的网络工具。拟南芥是一种广泛研究的模式植物，其转录组在各种组织、发育阶段和其他条件下都有大量的描述。通过对基因共表达关系的系统分析，可以重复使用这些数据来研究基因功能。我们从国家生物技术信息中心基因表达综合数据库收集了微阵列数据，确定了共表达基因模块并注释了模块功能。这些模块与实验/特征相关联，为表型提供了潜在的特征模块。根据关联推断出了新的热休克蛋白。高级模块网络分析表明，拟南芥网络可以进一步组织成 15 个元模块，并且叶绿体元模块与其他 14 个元模块的基因表达模式明显不同。与水稻转录组的比较显示出保留的模块和 KEGG 途径。所有模块基因信息都可以从 http://bioinformatics.fafu.edu.cn/arabi/ 上的在线工具获得。我们的研究结果为未来在拟南芥中进行基因发现提供了新的来源。
