Fwd: Fw: Epigenetic/bioinformatic inquiry!

[Pratibha]

Hello 

 

 We are studying the case of a variant that occurs in an intronic region of a gene, and the position of the variant coincides with elevated H3K27Ac signal (according to UCSC genome browser). Is there a tool within the browser that allows us to quantify this elevation in signal? 

 

Thank you for your help

Pratibha Nair
Senior Researcher
Centre for Arab Genomic Studies
P.O. Box 22252, Dubai
United Arab Emirates
 
Tel:  +971- 4 -398 6 777
Fax:  +971- 4 -398 0 999
CAGS Website:  www.cags.org.ae

[Christopher Lee]

Dear Pratibha,

Thank you for your question about quantifying the elevated H3K27Ac
signal for a specific region.

One tool you can use to accomplish this task is the Data Integrator
(http://genome.ucsc.edu/cgi-bin/hgIntegrator).

Once on the Data Integrator page, follow these steps to obtain
quantified signal information:

1) Under the "Select Genome Assembly and Region" section:
    a) Choose your genome and assembly of interest
    b) In the "region to annotate" text box paste in the genomic
        location of your variant of interest. If you do not know the
        specific location of your variant you may paste in a dbSNP
        rs number or gene name as well.

2) Under the "Configure Data Sources" section:
    a) From the "track group" drop down menu select "Regulation"
    b) From "track" select "ENCODE Regulation - Layered H3K27Ac.."
    c) From "subtrack" select the specific signal you are interested
        in quantifying. For a list of what each subtrack is you can
        review this page:
        http://genome.ucsc.edu/cgi-bin/hgTrackUi?&db=hg19&g=wgEncodeRegMarkH3k27ac
    d) Click the "Add" button

3) Under the "Output Options" section:
    a) Choose whether you would like to download the output to a file
        or view it as plain text in your browser.
    b) Click "Get output"

You should now have a file containing the chromosome, chromosome
start, chromosome end, and a list of values that represent
the data points in the H3K27Ac signal.

Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to gen...@soe.ucsc.edu. All messages
sent to that address are archived on a publicly-accessible forum. If your question
includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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