[Genome] finding information

[Brooke Rhead]

Hello Grace,

There are two tools you could use for extracting expression data from 
the Genome Browser: the Table Browser and the Gene Sorter.

The Table Browser can be used to extract data from a particular track in 
a particular location.  Before you start, however, you will need to 
figure out if the expression data in which you are interested are 
currently contained in one of our annotation tracks.  Look in the 
"Expression and Regulation" section of tracks, and click on the blue 
track names to read descriptions of the tracks.  When you find the 
expression data you wish to use, click on the "View table schema" link 
on the description page to get the name of the table underlying the track.

Now hit the "Tables" link in the blue bar at the top of the page.  This 
will take you to the Table Browser, where you can select the clade, 
genome, assembly, group (expression and regulation), track, and table to 
use.  For region, choose the position range of your gene of interest. 
Make any other selections you desire (such as entering an output file 
name), then hit "get output" to get the data in the selected table from 
the selected region.

The other tool that can extract expression data from the Genome Browser 
is the Gene Sorter.  (See the Gene Sorter User's Guide here: 
http://genome.ucsc.edu/goldenPath/help/hgNearHelp.html .)  To get to the 
Gene Sorter, click the "Gene Sorter" link in the blue bar at the top of 
the page.  Select your genome and assembly of interest and look up your 
gene(s) of interest using the search box.  Hit the "configure" button to 
turn on the display of data columns containing the expression data you 
want.  If you wish to limit the data displayed to only your two genes of 
interest, hit the "filter" button and paste the two gene names in the 
"Name - Gene Name/Select Gene" section (or, if using accession numbers, 
paste the identifiers in the appropriate filter box).  When you have all 
of the information displayed in the Gene Sorter the way you want, hit 
the "text" button to get the expression data in numerical format.

I hope one of these methods works for you.  If you need more 
information, please feel free to write back to this mailing list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group




Grace Gathungu wrote:
> Hello,
> 
> Is there a systematic method, or can you guide me on how to extract expression
> values for two distinct genes from the same source in a microarray data set
> that was previously published?
> 
> Grace Gathungu
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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