State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.
BMC Genomics. 2009 Nov 11;10:517. doi: 10.1186/1471-2164-10-517.
Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes.
The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database.
MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.
蒺藜苜蓿是一种模式豆科植物，其基因组目前正由一个国际联合组织进行测序。非生物胁迫，如盐胁迫，限制了植物的生长和作物的生产力，包括豆科植物。我们预计对蒺藜苜蓿的研究将为世界各地其他具有经济重要性的豆科植物提供启示。在这里，我们报告了一个名为 MtED 的数据库的开发，该数据库包含了基于 Affymetrix Medicago GeneChip 的蒺藜苜蓿根在时间过程盐胁迫实验中的基因表达谱。我们希望 MtED 将提供信息，以协助提高豆科植物的抗非生物胁迫能力。
我们用 180mM 氯化钠对蒺藜苜蓿根进行的微阵列实验的结果被存入 MtED 数据库。此外，还包括了微阵列探针集的序列和注释信息。MtED 提供了基于基因和基因盒本体论的功能类别分析，以及其他用于查询和检索查询结果、浏览途径和转录因子家族、显示代谢图谱以及比较和可视化表达谱的基于 Web 的工具。通过 BLAT 软件套件实现了将探针集映射到蒺藜苜蓿基因组和 In-Silico PCR 的实用程序，并通过 MtED 数据库提供了这些实用程序。
MtED 是用 PHP 脚本语言和 MySQL 关系数据库系统在 Linux 服务器上构建的。它有一个集成的 Web 界面，方便随时检查和解释微阵列实验的结果。它旨在帮助选择基因标记，以提高豆科植物的抗非生物胁迫能力。MtED 可在 http://bioinformatics.cau.edu.cn/MtED/ 获得。
