List Of Freely Available Eukaryotic Promoter Databases

Question

[Ranjita]

Could you suggest me which all databases represent the promoter region on a gene sequence. I want to represent promoter region on Glucokinase gene. Please help me in this regard.

[Neilfws]

Which organism? Eukaryote or prokaryote?

Answer 1

[Neilfws]

Assuming that you are interested in eukaryotes - probably humans - I'd start with the top hit from a Google search, which is the Eukaryotic Promoter Database.

Please provide more details (e.g. organism) if that's not what you want.

Answer 2

[razor]

Maybe http://doop.abc.hu. Not really up-to-date, but contains chordate and plant promoter collections. I am (was) responsible for it.

Answer 3

[Andrew Su]

BioMart's MartView has a pretty nice feature for downloading upstream sequences from genes.

Answer 4

[Pierre Lindenbaum]

Something like this?

[Giovanni M Dall'Olio]

The most recent article in the list is from 2008. How many of these are still online? :-(

Answer 5

[Casey Bergman]

Try the list of solutions and resources on Max Hauessler's Tregwiki on OpenWetWare

Answer 6

[Larry_Parnell]

You also need to look at what is being done with the VISTA project at Lawrence Berkeley Labs. The goal of VISTA is to identify distant-acting transcriptional enhancers in the human genome by coupling the identification of evolutionary conserved noncoding sequences with a moderate throughput mouse transgenesis enhancer assay.

Answer 7

[Mary]

Be sure to also explore the ENCODE data, in the regulation section, for several TFBS data sets that have new and interesting stuff. It is found in the UCSC Genome Browser, mostly on the human Mar 2006 assembly right now. I just saw the first mouse stuff come in, but it's pretty limited right now.

I second the VISTA suggestion as well. Their Enhancer Browser is a very neat project.

[Larry_Parnell]

Right on! I'm watching the video of Bradley Bernstein, (Associate Professor of Pathology, Harvard Medical School) give a talk at NHGRI's human genome 10th anniversary talks and this is precisely what he mentioned. Nice tissue-specificity @ ENCODE.

Answer 8

[Mohammad Reza Bakhtiarizadeh]

Hi i suggest you try Genomatix, it is very interesting database and also tools for promoter analysis. you can retrive promoter region, too. but at first you have to register by a academic email after that you can use it free for one week. i really suggest you see this site. regards

[Casey Bergman]

Though Genomatix does have free trial, it is a commercial solution and not freely available.

[Mohammad Reza Bakhtiarizadeh]

of course, I told you, you have to use a academic Email Address to register after that you can use this site for one week. i always use it. best

[Casey Bergman]

I read you answer fully and this is why I commented. Repeatedly using a free trial license does not a make a resource "freely available" (i.e. open access) and may in fact violate the terms of the license. I wouldn't recommend that any researcher use a multiple free trial offers if they intend to publish with the data/results procured in this manner.

[Mohammad Reza Bakhtiarizadeh]

Yes. you are right.