Hello Ilya,
The first thing to do is to identify a list of yeast genes that are stress
regulated. While we do not host experimental stress test data, it is possible
to look for the word "stress" in the sgdDescription table.
Here's how:
Use the Table Browser ("Tables" on the Blue Bar on the top of the page) with
the following settings:
clade: Other; genome: S. cerevisiae; assembly: Oct. 2003; group: Genes and Gene
Prediction Tracks; track: SGD Genes; table: sgdGene; region: genome;
filter: create
Under Linked Tables, click the box next to sacCer1.sgdDescription, then click
on "Allow Filtering Using Fields in Checked Tables". Now you can type *stress*
next to "description does match", and click submit.
Finally, under "output format" you can select sequence, if that's what you are
looking for, and follow the menus to indicate that you would like promoters
only, or you can select "selected fields from primary and related tables.",
which will take you to a second menu very similar to the Filter menu you just
used. Click "get output" to get your output.
For your second question, the answer is similar. You'll set things up as you
above, but in the Filter, change "name does match" and paste in your gene list.
Here is some documentation on the Table Browser, for your reference:
http://genome.ucsc.edu/cgi-bin/hgTables#Help
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
I hope this helps you get started with our tools. Please don't hesitate to
contact us again if you require further assistance.
Kayla Smith
UCSC Genome Bioinformatics Group
----- "Ilya Ioschikhes" <[email protected]> wrote:
> Hello,
>
>
>
> Please advise me how I may extract promoters of the yeast genes that
> are
> stress regulated.
>
>
>
> Also, I would need promoters of the genes that may be repressed by
> following
> proteins: ROX1, YFL052w, RDR1, NRG1, MGA1, RCS1.
>
>
>
> Thank you in advance for your help,
>
>
>
> ILYA IOSHIKHES, Ph.D.
>
> Associate Professor
>
> Ottawa Institute of Systems Biology (OISB) and
>
> Department of Biochemistry, Microbiology and Immunology (BMI)
>
> Faculty of Medicine
>
> University of Ottawa
>
> 4208 R. Guindon Hall
>
> 451 Smyth Road
>
> Ottawa ON, K1H 8M5
>
> Canada
>
> E-mail: [email protected]
>
> Tel. : +1 (613) 562-5800 ext. 4882
>
> Fax : +1 (613) 562-5370
>
> http://www.oisb.ca/members/member_Ilya_Ioshikhes.htm
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
