about promoter

[李远存]

hello, I come from China and I want to detect the CpG methylation located in promoters ,and now i am confused  by which chain do  the promoter located in?

can you tell me ?

[Matthew Speir]

Hello 李远存,

Thank you for your question about getting the promoter sequence for
genes in the UCSC Genome Browser. There are several ways that you can
get the DNA sequence for the promoters, and they are described in the
following FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download18.

If you already have the genomic coordinates for your promoters, you can
use the Table Browser to see if these promoter regions overlap with
potentially methylated regions. We have two tracks that have this
methylation information, the first is our predicted CpG islands track,
which contains computationally predicted CpG islands. For more
information on the CpGislands track, refer to the track description page
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cpgIslandExt. The
other track is the ENCODE Project DNA methylation tracks, which contain
regions that were experimentally predicted to be methylated. For more
information on this track, please refer to the track description page
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeDnaMethylSuper.
You can use the following settings to see if your promoter regions
overlap with the predicted CpG islands:

group: Regulation
track: CpG Islands
table: cpgIslandExt
region: you can paste in the promoter regions you're interested in by
clicking 'define regions'
output format: select you desired output format
output file: enter a file name to save your results to a file, or leave
blank to display results in the browser

Once you have selected the appropriate options, click 'get output'. You
can modify the track and table options above to the ENCODE methylation
tracks if you are interested in the information from those tracks.

I hope this is helpful. If you have any further questions, please reply
to genome...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your question
includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[李远存]

thank you so much for your letter, i never thought you would give me a reply. your information is very important to me and i know more about the CpG island now. UCSC is a very useful website and have been a great help to me in my research.

------------------ 原始邮件 ------------------

发件人: "Matthew Speir";

发送时间: 2013年11月22日(星期五) 上午10:42

收件人: "李远存"<3511...@qq.com>; "genome-mirror";

主题: Re: [genome-mirror] about promoter

to genome-mirror...@soe.ucsc.edu. All messages sent to that address are

archived on a publicly-accessible Google Groups forum. If your question

includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.