RegulonDB
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RegulonDB provides information on operon organization and regulation in E. coli. |
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Julio Collado-Vides |
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Contents
About RegulonDB
RegulonDB provides curated information on gene organization and regulation in E. coli. Current information is provided on the gene, operon and regulon level. Future expansion will include information on regulation beyond transcription initiation.
Content
The RegulonDB has information on the transcription units and the mechanical details of regulation of said units including: promoters and sigma factors, terminators and regulons. Additionally, the binding sites of the ribosome and transcriptional regulators are included. There is also information on the gene product. Additionally, the evidence for each fact is given in the cited references.
Textpresso at RegulonDB
RegulonDB uses Textpresso to allow mining of the literature corpus supporting RegulonDB annotations[1].
Using RegulonDB
Getting started with RegulonDB is relatively simple. Simply type in the gene, regulon or operon name that is desired. There is also a glossary that defines the terms that are used. Though there is a tutorial heading on the menu, there is really no tutorial--it's simply the glossary.
Browsing
Browsing RegulonDB has two main browsing functions: Genome Browser and Nebulon NetView.
To browse RegulonDB using Genome Browser, the user is presented with a graphical representation of the E. coli chromosome. Randomly clicking on a section gives the user a pictorial view of the selected section of the genome.
Browsing RegulonDB utilizing the Nebulon Net-View (though incredibly slow) gave an interesting view of the OxyR regulon. It allows one to search by gene name and graphically see the genes directly regulated by OxyR. An additional layer allows one to see which genes are regulated by those directly regulated by OxyR. Moving the mouse over a gene gave a pop-up window with a summary of information on this particular gene.
Searching
One can search Regulon DB by gene name, growth conditions, operon and regulon. In addition to searching by common gene name, synonym names also work (b number, older names, etc.).
The queries for searching by ECK# or gene name are shown below.
query by ECK# (http://regulondb.ccg.unam.mx/BGeneControllerServlet?key_id_org=ECK12&gene_id=ECK120000251)
query by gene name (http://regulondb.ccg.unam.mx/SearchListController?key_id_org=ECK12&object_id=edd&object_form=GN)
Usage examples
To search and test the database, I used OxyR. Here is a brief description about my experience:
First, I searched at the gene level. The page was well-orgainized and included some of the following: Name, Synonyms, Position, Nucleotide Sequence and links to other databases. The picture at the top allowed for clicking on surronding genes, as well as the promoter region of oxyR and oxyS.
Clicking on the promoter region took me to a new page that showed the operon of oxyR as well as the oxyR transcription unit. The information on this page gave me the +1, sigma factor and the sequence of the promoter, though I'm not sure what the difference between capital and lower cased letters mean.
Overall, interacting with the site was pretty straight-forward. I found the cited evidence to be correct. However, this was because I knew what the evidence was. The evidence is not directly linked to the fact-it's simply a list at the bottom.
Downloads
RegulonDB provides downloadable text files for promoters, transcription units, mRNAs etc. It also has experimental 5' end lists from Mendoza-Vargas et al (2009)[2]
Technology
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Rodríguez-Penagos, C et al. (2007) Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 8 293 PubMed
- ↑ Mendoza-Vargas, A et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE 4 e7526 PubMed
RegulonDB: a database on transcriptional regulation in Eschericia coli.
Huerta et al NAR 1998 vol 26. No. 1 pg 55-59. Full Text
RegulonDB (version4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
Salgado, H et al NAR 2004 Vol. 32 D303-D306. Full Text
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Salgado, H et al NAR 2006 Vol. 34 D394-3977. Full Text
External Links
RegulonDB URL: http://regulondb.ccg.unam.mx:80/index.html
