[Genome] Expression of brain-specific genes

[Rachel Harte]

Dear Dr. Paul Grossfeld,

If you are referring to human, we have the human Genomics Institute of
the Novartis Research Foundation (GNF) Atlas and human GNF Atlas 2
microarray expression data. You can view these by going to the track
controls below the Browser image and changing the visibility to turn on
the GNF Ratio (GNF Atlas 1) and GNF Atlas 2 tracks which are in the
"Expression and Regulation" group. If you click on the links above the
track controls, you will find the track descriptions and citations of the
publications for this data.

If you then copy the position of your region of interest into the
position/search box, you can view the data in this region. The Affy U95
track shows alignments of the sequences used for the design of probes for
the Affymetrix U95 GeneChip that was used for the GNF Ratio data and,
similarly, Affy GNF1H contains the alignments for a custom GeneChip
(GNF1H) that was used for the GNF Atlas 2 data. Sometimes several probeset
sequences are from the same region so, in the track display, the colouring
that you see in the GNF Ratio and GNF Atlas 2 tracks is a composite of that
for several probesets. You can see each one individually if you click on
an item in the track which will take you to a details page. The colouring
represents a log (base 2) ratio where red shows overexpression of a gene and
green is underexpression compared to reference. For this data, the
reference is the median of the medians of the replicates for all
tissues/cell lines that are non-cancerous.

You can also see which genes are represented by these probesets by turning
on some of the Genes tracks such as UCSC Genes (hg18, known Genes on
hg17), RefSeq, mRNA etc. By clicking on the Tables link in the top blue
bar you can query the tables that contain this data. If you select "All
Tables" as the group, you will see that there is a knownToAffyU95 and
knownToU95 and a knownToGnf1h which map the genes from the knownGene table
(UCSC Genes in hg18 and Known Genes in hg17) to the probeset sequences
from the Affymetrix U95 chip used for GNF Ratio and the GNF1H custom chip
used for GNF Atlas2 respectively. The mapping is such that for each known
gene it is mapped to the best overlapping probeset sequence that is
aligned to the same strand.

Another powerful tool for data mining is the Gene Sorter. You can reach
this by clicking on the "Gene Sorter" link on the top blue bar. There, you
can search for individual genes and then find other genes that have a
similar expression pattern in the GNF Atlas1 (GNF Ratio track) or GNF
Atlas2 data. The gene that you searched for will appear at the top and the
genes below it are related to the first one in order of decreasing
relatedness (in this case, similar expression patterns). The configure
button allow you to expand or reduce the number of data columns shown. By
default, only a subset of the tissues are shown for the expression data.
There is also a filter button which takes you to filter controls. You
could use to select for tissues that have a certain level of expression.

I hope that this helps you to get started. There are links to Help and FAQ
on the top blue menu bar of the Genome Browser pages. Also, please let us
know if you have further questions. In the future, please direct your Genome
Browser questions to our mailing list (genome at soe.ucsc.edu) for a faster
response - thanks.

Rachel

 Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


-------- Original Message --------
Date: 	Fri, 25 May 2007 17:04:53 GMT
From: 	pgrossfeld at UCSD.Edu
To: 	cbseweb at cbse.ucsc.edu



Dear Sir/Mam,
I am writing to seek your help.  I am interested in determining which genes
are expressed in the brain in a
specific chromosomal region:  chr11:120,472,551-133,693,850.  I understand you have an
atlas that
would have such information.  I do not have any experience in performing this kind of
analysis, and I
would deeply appreciate your helping me to use this powerful database.  Thank you in
advance!

Sincerely Yours,
Paul Grossfeld, M.D.
Assistant Adjunct Professor
Division of Pediatric Cardiology
UCSD School of Medicine
858-966-5855




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Communications & Human Resources
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