Search promoters of genes for the occurence of your pattern of interest

Original question:

> Dear
>
> My protein of interest is GR (Glucocorticoid receptor).
> I want to search for GR- inducible genes that contain a specific sequence
> on their promoter. I think that I can identify GR- dependent genes with
> Genevestigator.
> Can you propose me on line tools or ways so that when I have a list of GR
> dependent genes, to search among them which contain on their promoter the
> sequence that I am interested in.
>
> Thanks a lot in advance
>
> Kind regards

RSAT's tool dna-pattern can help you further: http://rsat.scmbb.ulb.ac.be/rsat/ For your interest, more on such tools on our wiki the page Transcription-factor_binding_site_discovery.

First you need to obtain the sequence of your list of genes, using Biomart

1. copy paste the identifiers
2. Go to http://www.biomart.org/biomart/martview/ and select the correct species.
3. So, as dataset, choose Ensembl Genes 69, and choose in the dropdown box that appears below your species.
4. First we set the filter (in the left bar): namely genes with the identifier that you provide (click on filters -> Gene -> ID list limit --> choose the correct Affy identifier)
5. Click on the Count button on the top bar to see how many genes are recognised/retrieved by the filter
6. If everything is allright, go to Attributes (in the left bar), and click on 'Sequences' in the middle pane. Choose 'Flank (Gene)', and enter how many bases you want to analyse in the region before the start of the gene. I propose 2kb is a good starting point.
7. Finally, click on the Results button in the top bar and click Go.

That list of promoters you can feed into DNA-pattern, together with the string/pattern you are interested in. dna-pattern tool is listed in the left bar. See http://rsat.scmbb.ulb.ac.be/rsat/