[Genome] Use of ENCODE project data

[Ann Zweig]

Hello Philip,

	I would suggest you start at our ENCODE portal: 
http://genome.ucsc.edu/ENCODE/   From here you will have access to all 
of the published ENCODE data.

- You can view these data in the genome browser: 
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr7:115,404,472-117,281,897&encodeRegions=full

- You can download ENCODE data tables: 
http://hgdownload.cse.ucsc.edu/goldenPath/encode/index.html

- You can perform queries on the ENCODE data tables: 
http://genome.ucsc.edu/cgi-bin/hgTables


	There is ENCODE data available on two human assemblies: May 2004 (UCSC 
hg17, NCBI Build 35), and  Jul. 2003 (UCSC hg16, NCBI Build 34).

	To become familiar with the data that are available, start with the 
genome browser.  Navigate to the hg17 assembly and scroll down the page 
to the track controls until you start to see the ENCODE sections.  For 
example, when you get to the section entitled "ENCODE Transcript 
Levels", you will see the following tracks:

   Affy RNA Signal
   Affy Transfrags
   BU First Exon
   Riken CAGE
   Stanf Promoter
   Stanf RTPCR
   Yale MAS RNA
   Yale MAS TAR
   Yale RNA
   Yale TAR

	Change the visibility of the tracks to see them in the display.  Or, 
click on the track name to link to a description page that gives many 
details about the track, including Methods, Verification, Credits, and 
References.

	Once you become familiar with the available data, I think it will 
become clear to you how to find the functional elements you are looking for.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Philip M Terry wrote:
> Hello,
> 
> May I ask the following question concerning the ENCODE project:
> 
> I am a novice with respect the the ENCODE project.  I would like to
> find/locate (in the human genome) functional elements such as transcription
> binding site locations, promoter regions, nucleosome poor regions, etc. Can
> you suggest how I should proceed?
> 
> Sincerely,
> Philip M. Terry, PhD
> University of Nebraska-Lincoln
> 
> _______________________________________________
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