Kudo Toru, Terashima Shin, Takaki Yuno, Tomita Ken, Saito Misa, Kanno Maasa, Yokoyama Koji, Yano Kentaro
Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
Plant Cell Physiol. 2017 Jan 1;58(1):e1. doi: 10.1093/pcp/pcw208.
Publicly available microarray-based transcriptome data on plants are remarkably valuable in terms of abundance and variation of samples, particularly for Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Here, we introduce the web database PlantExpress (http://plantomics.mind.meiji.ac.jp/PlantExpress/) as a platform for gene expression network (GEN) analysis with the public microarray data of rice and Arabidopsis. PlantExpress has two functional modes. The single-species mode is specialized for GEN analysis within one of the species, while the cross-species mode is optimized for comparative GEN analysis between the species. The single-species mode for rice is the new version of OryzaExpress, which we have maintained since 2006. The single-species mode for Arabidopsis, named ArthaExpress, was newly developed. PlantExpress stores data obtained from three microarrays, the Affymetrix Rice Genome Array, the Agilent Rice Gene Expression 4x44K Microarray, and the Affymetrix Arabidopsis ATH1 Genome Array, with respective totals of 2,678, 1,206, and 10,940 samples. This database employs a ‘MyList’ function with which users may save lists of arbitrary genes and samples (experimental conditions) to use in analyses. In cross-species mode, the MyList function allows performing comparative GEN analysis between rice and Arabidopsis. In addition, the gene lists saved in MyList can be directly exported to the PODC database, which provides information and a platform for comparative GEN analysis based on RNA-seq data and knowledge-based functional annotation of plant genes. PlantExpress will facilitate understanding the biological functions of plant genes.
就样本的丰富性和多样性而言，公开可用的基于微阵列的植物转录组数据具有极高的价值，尤其是对于水稻（Oryza sativa）和拟南芥（Arabidopsis thaliana）。在此，我们介绍网络数据库PlantExpress（http://plantomics.mind.meiji.ac.jp/PlantExpress/），它是一个利用水稻和拟南芥的公共微阵列数据进行基因表达网络（GEN）分析的平台。PlantExpress有两种功能模式。单物种模式专门用于一个物种内的GEN分析，而跨物种模式则针对两个物种之间的比较GEN分析进行了优化。水稻的单物种模式是OryzaExpress的新版本，自2006年以来我们一直在维护。拟南芥的单物种模式名为ArthaExpress，是新开发的。PlantExpress存储了从三种微阵列获得的数据，即Affymetrix水稻基因组阵列、安捷伦水稻基因表达4x44K微阵列和Affymetrix拟南芥ATH1基因组阵列，样本总数分别为2678个、1206个和10940个。该数据库采用了“我的列表”功能，用户可以保存任意基因和样本（实验条件）的列表以供分析使用。在跨物种模式下，“我的列表”功能允许在水稻和拟南芥之间进行比较GEN分析。此外，保存在“我的列表”中的基因列表可以直接导出到PODC数据库，该数据库基于RNA测序数据和植物基因的基于知识的功能注释，提供信息和比较GEN分析的平台。PlantExpress将有助于理解植物基因的生物学功能。
