[Genome] Questions about GNF Atlas2 Table

[Kayla Smith]

Hello Wenjun,

This previously answered mailing list question has some information which
will help you:
http://www.soe.ucsc.edu/pipermail/genome/2005-June/007891.html

The number of items in hgFixed.gnfHumanAtlas2Median is 44775, and the
number of items in hg18.gnfAtlas2 is 34926.   Not all probes successfully
map to the genome.

Here is another previously answered mailing list question about finding
expressed genes in each tissue:
http://www.soe.ucsc.edu/pipermail/genome/2005-April/007245.html

This should help you get started.  If you have further questions, please
don't hesitate to contact us again.

Kayla Smith
UCSC Genome Bioinformatics Group

On Tue, 8 Apr 2008, He Wenjun wrote:

> Dear Sir or Madam,
>
> I'm using the GNF Atlas2 data  from your Table Browser to do some research.
>
> I am confused about some procedures taken to build the database, and I can't
> find the relevant information anywhere.
>
> For example,
> 1). how did you relate the data from GNFAtlas to the USCS Known Gene?
> 2). Why the number of items in hgFixed.gnfHumanAtlas2Median is less than
> gnfAtlas2?
>
> 3). I wanna select some highly expressed tissue-specific genes. What cut-off
> value or method should I take according to the expScores?
>
> If it is possible, could you please give me a detailed describe
> about processes taken to build the GNF Atlas2 database? That would help me a
> lot.
>
> Your help wil be appreciated very much.
>
> Yours sincerely,
> Wenjun He
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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>