COXPRESdb: a database to compare gene coexpression in seven model animals.
COXPRESdb: a database to compare gene coexpression in seven model animals.
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DOI：
10.1093/nar/gkq1147
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Kinoshita K
中科院分区：
文献类型：
--
作者：
Obayashi T;Kinoshita K
公开的共表达基因集数据库是各种实验研究的宝贵资源，包括用于功能鉴定的基因靶向，以及用于研究调控机制或蛋白质-蛋白质相互作用网络。虽然共表达基因数据库在植物生物学领域越来越受欢迎，但与动物数据相关的数据库却相当有限，这可能是由于共表达数据的可靠性较低。原始COXPRESdb（共表达基因数据库）（http：coxpresdb.jp）代表人和小鼠的共表达关系。在这里，我们报告这个数据库的更新，特别是专注于提高动物基因共表达数据的可靠性。为此，我们实施了一种新的可比较的共表达测量，相互排名，包括其他五种动物物种，大鼠，鸡，斑马鱼，苍蝇和蜻蜓，以评估共表达的保守性，并将不同层次的组学数据添加到基因的集成网络中。共表达的比较是提高基因共表达可靠性的关键概念，不同信息的整合可以减少信息中固有的噪声。COXPRESdb具有表达基因网络的功能，可以帮助研究人员阐明广泛动物物种中基因的功能和调控网络。
Publicly available databases of coexpressed gene sets are a valuable resource for a wide variety of experimental studies, including gene targeting for functional identification, and for investigations of regulatory mechanisms or protein–protein interaction networks. Although coexpressed gene databases are becoming more and more popular in the field of plant biology, those with animal data are rather limited, possibly due to the lower reliability of the coexpression data. The original COXPRESdb (coexpressed gene database) (http://coxpresdb.jp) represented the coexpression relationship for human and mouse. Here, we report updates of this database that especially focus on the enhancement of the reliability of gene coexpression data in animals. For this purpose, we implemented a new comparable coexpression measure, Mutual Rank, included five other animal species, rat, chicken, zebrafish, fly and nematoda, to assess the conservation of coexpression, and added different layers of omics data into the integrated network of genes. Comparison of coexpression is a key concept to enhance the reliability of gene coexpression, and the integration of different information can reduce the noise inherent in the information. With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species.
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