OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice
OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice
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DOI：
10.1093/pcp/pcq195
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发表时间：
2011-02-01
影响因子：
4.9
通讯作者：
Yano, Kentaro
中科院分区：
文献类型：
--
作者：
Hamada, Kazuki;Hongo, Kohei;Yano, Kentaro
基因表达谱的相似性为理解基因的生物学功能、生物过程和与基因相关的代谢途径提供了重要线索。基因表达网络(Gen)是同时掌握基因间表达谱相似性的理想选择。在基因构建中，皮尔逊相关系数(PCC)被广泛用作评价基因对表达谱相似性的指标。然而，计算所有基因对的PCC需要大量的时间和计算机资源。基于对应分析，我们提出了一种新的构造Gen的方法，即使在一般计算环境下，对于大规模的表达式数据，该方法也只需最少的时间。此外，我们的方法不需要任何先验参数来去除数据集中的样本冗余。使用这种新方法，我们从存储在公共数据库中的大规模基因芯片数据中构建了水稻基因。然后，我们收集并整合了公共和不同数据库中的各种主要水稻组学注释。整合的信息包括基因组、转录组和代谢途径的注释。因此，我们开发了用于浏览氏族的集成数据库OryzaExpress，它具有交互式和图形查看器以及主要组学注释(http://riceball.lab.nig.ac.jp/oryzaexpress/).通过整合来自ATTED-II的拟南芥基因数据，OryzaExpress还允许我们比较水稻和拟南芥之间的基因。因此，OryzaExpress是一个全面的水稻数据库，它从植物科学的各个角度利用了强大的组学方法，并导致了系统生物学。
Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology.