An expression database for roots of the model legume Medicago truncatula under salt stress.
An expression database for roots of the model legume Medicago truncatula under salt stress.
复制标题
盐胁迫下模式豆科蒺藜苜蓿根的表达数据库
DOI：
10.1186/1471-2164-10-517
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发表时间：
2009-11-11
期刊：
影响因子：
4.4
通讯作者：
Wang T
中科院分区：
文献类型：
--
作者：
Li D;Su Z;Dong J;Wang T
背景
蒺藜苜蓿是一种模式豆科植物，国际联盟目前正在对其基因组进行测序。非生物胁迫如盐胁迫限制植物生长和作物生产力，包括豆科植物的生长和生产力。我们预计，对蒺藜豆的研究将为世界各地其他具有重要经济意义的豆科植物提供线索。在这里，我们报告了一个名为 MtED 的数据库的开发，该数据库包含基于使用 Affymetrix Medicago GeneChip 的时程盐胁迫实验的 M. truncatula 根的基因表达谱。我们希望 MtED 能够提供信息来帮助提高豆类的非生物胁迫抗性。
描述
我们在 180 mM 氯化钠下对蒺藜根进行微阵列实验的结果已保存在 MtED 数据库中。此外，还包括有关微阵列探针组的序列和注释信息。 MtED 提供基于 Gene 和 GeneBins Ontology 以及其他基于 Web 的工具的功能类别分析，用于查询和检索查询结果、浏览通路和转录因子家族、显示代谢图以及比较和可视化表达谱。 BLAT 软件套件实现了将探针组映射到蒺藜 M. truncatula 基因组和 In-Silico PCR 等实用程序，这些软件套件也可通过 MtED 数据库获得。
结论
MtED 采用 PHP 脚本语言构建，并作为 Linux 服务器上的 MySQL 关系数据库系统。它有一个集成的网络界面，可以方便地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类的非生物胁迫抗性。 MtED 可在 http://bioinformatics.cau.edu.cn/MtED/ 获取。
Background
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.
Description
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.
Conclusion
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/.
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