The Rice Oligonucleotide Array Database: an atlas of rice gene expression.
The Rice Oligonucleotide Array Database: an atlas of rice gene expression.
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DOI：
10.1186/1939-8433-5-17
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发表时间：
2012-07-19
期刊：
影响因子：
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通讯作者：
Ronald PC
中科院分区：
文献类型：
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作者：
Cao P;Jung KH;Choi D;Hwang D;Zhu J;Ronald PC
微阵列技术促进了高通量的基因表达分析。然而，水稻基因表达分析平台的多样性阻碍了有效的分析。需要广泛整合来自不同平台的微阵列数据的工具。在这项研究中，我们开发了水稻寡核苷酸阵列数据库(ROAD，http://www.ricearray.org))，以探索1,867个公开可用的水稻微阵列杂交材料的基因表达。该道路的用户友好的网络界面和各种可视化工具促进了使用基因和微阵列元素识别提取基因表达谱。这条道路支持对不同组织和发育阶段表达的基因进行荟萃分析。共表达分析工具提供了在一般、非生物和生物胁迫条件下基因之间共同调控的信息。此外，功能分析工具，如基因本体论和KEGG(京都基因和基因组百科全书)正字法，被嵌入在道路中。这些工具有助于在一系列查询基因中识别有意义的生物模式。水稻寡核苷酸阵列数据库提供了所有水稻基因的全面基因表达谱，将为水稻和其他草本植物的研究人员提供有用的资源。本文的在线版本(DOI：10.1186/1939-8433-5-17)包含补充材料，可供授权用户使用。
Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. In this study, we developed the Rice Oligonucleotide Array Database (ROAD,http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species. The online version of this article (doi:10.1186/1939-8433-5-17) contains supplementary material, which is available to authorized users.