ODB: a database of operons accumulating known operons across multiple genomes.
ODB: a database of operons accumulating known operons across multiple genomes.
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DOI：
10.1093/nar/gkj037
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发表时间：
2006-01-01
影响因子：
14.9
通讯作者：
Kanehisa, Minoru
中科院分区：
文献类型：
--
作者：
Okuda, Shujiro;Katayama, Toshiaki;Kawashima, Shuichi;Goto, Susumu;Kanehisa, Minoru
操纵子结构在原核生物的共同调节中发挥着重要作用。尽管现在有超过 200 个完整的基因组序列，但提供全基因组操纵子信息的数据库仅限于某些特定基因组。因此，我们开发了ODB（Operon DataBase），它提供了许多完整基因组中已知操纵子的数据检索系统。另外，还提供了在已知操纵子方面保守的推定操纵子。我们数据库的当前版本包含 50 多个基因组中的约 2000 个已知操纵子信息以及 200 多个基因组中的约 13000 个推定操纵子信息。该系统集成了四种类型的关联：基因组背景、从微阵列数据获得的基因共表达、生物途径中的功能链接以及跨基因组的基因顺序的保守。这些关联是组织操纵子的基因的指标，这些指标的组合使我们能够预测更可靠的操纵子。此外，我们的系统使用从文献中获得的已知操纵子信息来验证这些预测。该数据库集成了已知的基于文献的信息和基因组数据。此外，它还提供了操纵子预测工具，使该系统对生物信息学研究人员和实验生物学家都很有用。我们的数据库可通过以下网址访问。
Operon structures play an important role in co-regulation in prokaryotes. Although over 200 complete genome sequences are now available, databases providing genome-wide operon information have been limited to certain specific genomes. Thus, we have developed an ODB (Operon DataBase), which provides a data retrieval system of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The current version of our database contains about 2000 known operon information in more than 50 genomes and about 13 000 putative operons in more than 200 genomes. This system integrates four types of associations: genome context, gene co-expression obtained from microarray data, functional links in biological pathways and the conservation of gene order across the genomes. These associations are indicators of the genes that organize an operon, and the combination of these indicators allows us to predict more reliable operons. Furthermore, our system validates these predictions using known operon information obtained from the literature. This database integrates known literature-based information and genomic data. In addition, it provides an operon prediction tool, which make the system useful for both bioinformatics researchers and experimental biologists. Our database is accessible at .
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