RegulonDB

You can help EcoliWiki by editing the content of this page. For information about obtaining editing privileges, see E._coli_Wiki:Membership

RegulonDB
Who:	Julio Collado-Vides
What:	RegulonDB provides information on operon organization and regulation in E. coli.
Where:	RegulonDB
Updates	Version 5.0 was released early 2006.
Upcoming events	link to event calendar, if applicable
Web Services

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 a brief introduction as to what the goals of the database is. 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."

Using RegulonDB

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.

Discussion

Trackbacks

This feature is not yet functional

• $4$5: [$2 $1]

References

RegulonDB: a database on transcriptional regulation in Eschericia coli.
Huerta et al NAR 1998 vol 26. No. 1 pg 55-59.

RegulonDB (version4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.
Salgado et al NAR 2004 Vol. 32 D303-D306.

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Salgado et al NAR 2006 Vol. 34 D394-3977.

External Links

RegulonDB

Discussion of RegulonDB on other websites

CiteUlike