[Genome] Expression for human genes

[Kayla Smith]

Isabelle,

Use the following settings in the table browser to retrive the data you 
  are interested in:

clade: Vertebrate
genome: Human
assembly: Mar. 2006
group: mRNA and EST Tracks
track: Spliced ESTs
table: intronEst
region: (specify the genomic position you are interested in here.  Note 
that there are about 4 million items in this table, so choosing "genome" 
here may be overwhelming)
output format: all fields from selected table
click "get output" for your results.


You may also download tables by clicking on the downloads link
("downloads" on the blue bar on the left-hand side of the main page),
clicking on Human, and then clicking on "Annotation database".

You are looking for the file:  intronEst.txt.gz

Note that in the methods section of the details page for ESTs, we
mention: "When a single EST aligned in multiple places, the alignment
having the highest base identity was identified. Only alignments having
a base identity level within 0.5% of the best and at least 96% base
identity with the genomic sequence were kept."

Additionally, since you mention that you are studying gene expression, I 
want to point out that we have some gene expression data availible in 
our browser which may be of use to you.  In the Human Genome Browser, we 
have GNF Atlas data and also some Affymetrix Human Exon array data.  You 
can find these tracks under the "Expression and Regulation" section of 
the track controls of the browser.

I hope this information is helpful to you.  Please don't hesitate to
contact us again if you require more assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Isabelle Dupanloup wrote:
> Hi there,
> 
> I would like to study the expression of human genes using ESTs/cDNAs.
> I saw that you make available on your website the coordinates of
> ESTs/cDNAs mapping to the human genome (defined as blat hits).
> My question is about the best way to retrieve this info using your table
> browser 
> Group: mRNA and EST track
> What are the optimal choices for 
> 1) track ?
> 2) table ?
> There are many possibilities in there.
> What I need is the best mapping of ESTs/cDNAs to the human genome.
> Could you help me to find the way to get it ?
> 
> Thank you very much in advance.
> And thank you also for your very nice tool.
> 
> Isabelle
> 
> -------------------
> Isabelle Dupanloup PhD
> Computational and Molecular Population Genetics Group Baltzerstrasse 6
> 3012 Bern Switzerland
> Tel: +41 31 631 45 49
> Fax: +41 31 631 48 88
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome