Question: Transcription Factor Binding Sites Database For Bacteria?
11
gravatar for Magdalena
8.7 years ago by
Magdalena230
Magdalena230 wrote:

Is there a database which provides information on transcription factor binding sites in PROKARYOTES? In this forum I have seen recommendations for JASPAR and TRANSFAC, but both of them seem to include data on eukaryotic TFs only.

More specifically, I am looking for a resource where I can find recognition sequences of sigma factors. E. coli would be great, more taxa even greater.

Thanks for your help!

ADD COMMENTlink modified 15 months ago by zhuofei.xu10 • written 8.7 years ago by Magdalena230
12
gravatar for Farhat
8.7 years ago by
Farhat2.9k
Pune, India
Farhat2.9k wrote:

Prodoric (http://www.prodoric.de/) is a good database for Prokaryotic gene regulation. It covers quite a few taxa including E. coli.

ADD COMMENTlink written 8.7 years ago by Farhat2.9k
9
gravatar for Casey Bergman
8.7 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Try RegulonDB and/or EcoCyc.

ADD COMMENTlink written 8.7 years ago by Casey Bergman18k
7
gravatar for Ian
8.7 years ago by
Ian5.6k
University of Manchester, UK
Ian5.6k wrote:

You might find this reference interesting as general review of TF databases (inc. bacterial):

Charoensawan V, Wilson D, Teichmann SA. Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res. 2010 Nov 1;38(21):7364-77. PubMed PMID: 20675356

ADD COMMENTlink written 8.7 years ago by Ian5.6k
6
gravatar for Michael Dondrup
8.7 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

If you are working with Corynebacteria, E. coli, or Mycobacterium tubercolosis try CoryneRegNet

RhizoRegNet is a similar database for Rhizobia

One of the coolest features of the RegNets is the JavaApplet for rendering regulatory networks. Click the GraphVis button, after searching for a regulatory gene.

ADD COMMENTlink written 8.7 years ago by Michael Dondrup47k
5
gravatar for Rayna
8.7 years ago by
Rayna250
Paris/Munich
Rayna250 wrote:

If you work with E. coli in particular, you can find a great amount of very useful data here: RegulonDB download page. Hope this helps.

ADD COMMENTlink written 8.7 years ago by Rayna250
4
gravatar for Simon Cockell
8.7 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

DBTBS is a database of transcription factors for Bacillus subtilis.

ADD COMMENTlink written 8.7 years ago by Simon Cockell7.3k
2
gravatar for sefakilic
4.8 years ago by
sefakilic20
United States
sefakilic20 wrote:

Try CollecTF, a database of transcription factor binding sites (TFBS) in the Bacteria domain.

ADD COMMENTlink modified 3 months ago by RamRS25k • written 4.8 years ago by sefakilic20

CollecTF is awesome.

ADD REPLYlink written 4.8 years ago by pld4.8k
1
gravatar for Michael Dondrup
8.7 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

And here is a new algorithm for de-novo prediction of TFBS in prokaryotes. They also use some of the databases mentioned here before as sources for their validation.

Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes Shaoqiang Zhang, Shan Li, Phuc T Pham and Zhengchang Su

ADD COMMENTlink modified 3 months ago by RamRS25k • written 8.7 years ago by Michael Dondrup47k
1
gravatar for ced.lefrancq
6.5 years ago by
ced.lefrancq10
ced.lefrancq10 wrote:

I have more or less the same problem. Nevertheless, I found the model organism of my bacteria and I can see the information on it. The big deal is I can just see the information and search the similar sequence manually but not compare my file including my genome and obtain the results automatically. That take very long time and is not possible of all do. Someone has a method to do this?

ADD COMMENTlink written 6.5 years ago by ced.lefrancq10

you should probably rephrase this as a new question - I'm afraid no one is going to see it down here.

ADD REPLYlink written 6.5 years ago by Simon Cockell7.3k
0
gravatar for zhuofei.xu
15 months ago by
zhuofei.xu10
zhuofei.xu10 wrote:

RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics.

quite awesome!

ADD COMMENTlink written 15 months ago by zhuofei.xu10
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