Plant Biology Division, the Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
BMC Bioinformatics. 2009 Dec 22;10:441. doi: 10.1186/1471-2105-10-441.
Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose.
The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(R) Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/.
The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.
豆类（豆科或蝶形花科）在农业中起着重要作用。模式豆科植物蒺藜苜蓿的转录组学研究有助于帮助制定关于豆科基因作用的假说。随着大量组织、细胞类型、生长条件和应激处理的公共可用的 Affymetrix GeneChip 蒺藜苜蓿基因组 Array GeneChip 数据的快速增长，豆科研究界希望有一种有效的生物信息学系统来帮助通过功能基因组学解释蒺藜苜蓿基因组。为此，我们开发了蒺藜苜蓿基因表达图谱（MtGEA）网络服务器。
蒺藜苜蓿基因表达图谱（MtGEA）网络服务器是分析蒺藜苜蓿转录组的集中平台。目前，该网络服务器托管了来自 156 个 Affymetrix GeneChip（R）蒺藜苜蓿基因组芯片的基因表达数据，涵盖了广泛的发育和环境条件。该服务器能够灵活、多方面地分析转录数据，并提供有关基因的一系列其他信息，包括不同类型的注释和与基因组序列的链接，这有助于用户制定有关基因功能的假说。可以使用 Affymetrix 探针识别号、DNA 序列、基因名称、自然语言中的功能描述、GO 和 KEGG 注释术语以及 InterPro 域号来访问转录本数据。还可以通过共表达或差异表达分析发现转录本。已经实现了灵活的工具来选择实验子集，并可视化和比较多个基因的表达谱。可以以表格形式部分或全部下载数据，该表格形式与常见的分析和可视化软件兼容。该网络服务器将定期更新，以纳入新的基因表达数据和基因组注释，并可在以下网址访问：http://bioinfo.noble.org/gene-atlas/。
MtGEA 网络服务器拥有管理良好的丰富数据集，并提供了网络平台中的数据检索和分析工具。它已被证明是植物生物学家从多个方面有效和高效地识别蒺藜苜蓿感兴趣的转录本、制定关于基因功能的假说以及从系统的角度整体解释蒺藜苜蓿基因组的强大资源。
