RegulonDB (version 4.0):: transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
RegulonDB (version 4.0):: transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
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DOI：
10.1093/nar/gkh140
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Collado-Vides, J
中科院分区：
文献类型：
--
作者：
Salgado, H;Gama-Castro, S;Collado-Vides, J
RegulonDB是主要国际维护的原始文献的主要数据库，具有关于大肠杆菌K-12中转录调控网络的元件和相互作用的实验知识。这包括关于操纵子组织及其分解成转录单位（TU）、启动子及其α类型、特定转录调节因子（TR）的结合位点、其组织成“调节短语”、TR的活性和非活性构象以及终止子和核糖体结合位点的机械信息。该数据库的补充与明确标记的计算预测的TU，启动子和TR的结合位点。目前的版本已扩大到包括信息以外的具体机制，旨在收集不同的生长条件和相关的诱导和/或抑制基因。RegulonDB现在与Swiss-Prot、微阵列数据库和一套程序连接，用于分析和可视化微阵列实验。我们提供了RegulonDB中包含的生物学知识的摘要，并描述了数据库设计中的主要变化。RegulonDB可通过网址http://www.cifn.unam.mx/Computational-Biology/regulondb/访问。
RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their a type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational-Biology/regulondb/.