Database for promoters? - How can I find out information about promoters as opposed to coding se (Jun/18/2008 )

One thing that's always frustrated me is that it seems to be really difficult to search for information about promoters. For example, when cloning, I'm often interested in knowing either in which tissues the promoter I am using is active, or what different promoters might be active in the tissue I'm targeting, and their relative strengths. Sometimes I want to find the wild-type sequence or chromosomal location, but I find the NCBI Nucleotide search results basically worthless. No matter how stringent I set my search limits, I seem to only end up finding sequence info on transcripts or genes.

So much of what I know about various promoters is based on word-of-mouth, or hands-on experience. I've also spent quite a bit of time poring over publications trying to glean information, but this approach is quite inefficient, and often I can't find out the information I'd like to know, such as which transcription factors they require, or where they are located chromosomally relative to their corresponding gene or genes. I realise that this information isn't always available, but some promoters are reasonably well-studied, and this information must exist for them.

How does everyone here get information about promoters? What I'd like to find is some sort of online database of promoters, where one could search based on criteria such as tissue specificity, relative strength, transcription factors, etc.

Is this just a pipe dream?

Ginger

hi ginger,

i don't know what organism you're working with. for plants there are different promoter databases. one of them is plant care at http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

there are some others, one at the server of ucsc which seems to be really good, but as i tell you, it depends on the organism you're using. for mammals i have no idea...

hi ginger,

i don't know what organism you're working with. for plants there are different promoter databases. one of them is plant care at http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

there are some others, one at the server of ucsc which seems to be really good, but as i tell you, it depends on the organism you're using. for mammals i have no idea...

hi again,

there's this old topic that might help you

http://www.protocol-online.org/forums/inde...?showtopic=3072

Hi Ginger,

I agree that searching NCBI for promoter sequences is a frustrating experience. I would say that promoters are the least annotated feature in the genome databases compared to other sequence features. Despite that, there are many alternative ways of obtaining promtoer sequences of genes.

Since genome sequencing has been completed or near completed for many organisms and their genes are well annotated and we also know that almost all promoters are located immediated upstream transcription start site. Based on these information we are able to retrieve putative promoter sequences from genome database. What you need to know is the name of the gene and the transcription start site or the start of the first exon. I found Ensembl provides the most convienent tool for such purpose as i have noted here.

Regarding promoter database, you can look into The Eukaryotic Promoter Database: an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.

This topic has been discussed many times and you can find those threads by using this search link.

Hope that helps.