RegulonDB (version 4.0):: transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

被引:184
作者
Salgado, H [1 ]
Gama-Castro, S [1 ]
Martínez-Antonio, A [1 ]
Díaz-Peredo, E [1 ]
Sánchez-Solano, F [1 ]
Peralta-Gil, M [1 ]
Garcia-Alonso, D [1 ]
Jiménez-Jacinto, V [1 ]
Santos-Zavaleta, A [1 ]
Bonavides-Martínez, C [1 ]
Collado-Vides, J [1 ]
机构
[1] Univ Nacl Autonoma Mexico, CIFN, Program Computat Genom, Cuernavaca 62100, Morelos, Mexico
关键词
D O I
10.1093/nar/gkh140
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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/.
引用
收藏
页码:D303 / D306
页数:4
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