Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
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DOI：
10.1007/s10265-010-0333-6
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发表时间：
2010-05-01
影响因子：
2.8
通讯作者：
Kinoshita, Kengo
中科院分区：
文献类型：
--
作者：
Obayashi, Takeshi;Kinoshita, Kengo
基因共表达分析是预测基因功能和/或鉴定与查询基因功能相关的基因的有力方法。基因共表达分析的基本思想是具有相似功能的基因在许多不同条件下应该具有相似的表达模式。这种方法现在被许多实验研究人员广泛使用，特别是在植物生物学领域。在这篇综述中，我们将总结最近成功的例子，通过使用我们的基因共表达数据库，ATTED-II。具体来说，这些例子将描述新基因的鉴定，如复杂蛋白质的亚基，代谢途径中的酶和转运蛋白。此外，我们还将讨论一种新的细胞间信号传导因子的发现以及转录因子与其靶基因之间的新的调控关系。在ATTED-II中，我们提供了两种基本的基因共表达视图，基因列表视图和基因网络视图，它们可以分别用作指导基因方法和缩小方法。此外，我们将讨论各种类型的基因集的共表达的有效性。
Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.