[Genome] Questions on gene expression data

[Kayla Smith]

William,

Thank you for your compliments on the Genome Browser.

The most popular expression data on the Genome Browser is the GNF Atlas 
2 expression data.  This data represents 79 human tissues, 61 mouse 
tissues or 44 rat tissues run on affymetrix arrays.  I'll give you some 
insight into this data set.

There are two ways to browse this expression data on our website.  One 
is to turn on the gnfAtlas2 track in the browser.  This will let you see 
expression values for various tissues on genomic intervals of your 
choice.   The other is to use the Gene Sorter (there is a link for "Gene 
Sorter" on the blue bar on the top of the main page) which shows you 
expression values for tissues for each gene.  One particularly useful 
feature of the Gene Sorter is that you can sort by expression pattern.

On the top of the Gene Sorter's gnfAtlas2 column, you can click where 
you see the names of the tissues.  This will take you to more 
information on the gnfAtlas2 data (You can also click on the top of the 
column for other types of expression data, such as Gladstone, GNF U74A, 
arbeitman, etc.). Here is the link (for human) for your convenience:

http://genome.ucsc.edu/cgi-bin/hgNear?near.do.colInfo=gnfHumanAtlas2

In the "Methods" section you'll see:

"When calculating expression ratios, the overall expression level in the 
denominator was calculated by first taking the median of replicates for 
each non-cancerous tissue, and then taking the median of these medians."

That means that up- and down-regulation of a gene in a tissue is 
relative to the the median of other tissues.  For example a red square 
in the "heart" column of the gene sorter for the gene "ACTC" means that 
this gene is up-regulated in heart compared to how it is expressed in 
the other tissues.  You are correct that the data is displayed such that 
green represents downregulation and red represents upregulation.


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

Kayla Smith
UCSC Genome Bioinformatics Group


William Grisham wrote:
> Hi,
> 
> I am teaching an undergraduate neuroscience class and using the UCSC 
> Genome Browser as a tool in instruction.
> 
> We are interested in the expression data.  I took a class from Open 
> Helix a couple of years ago and was led to believe that if the box for 
> a given tissue was red, the gene was upregulated.  If the box is green, 
> it is downregulated.
> 
> My question is up or down regulated relative to what?
> 
> Many thanks for the UCSC Genome Browser--it has been a terrific 
> teaching tool!
> 
> Sincerely,
> 
> William Grisham, Ph.D.
> Department of Psychology
> UCLA
> 1285 Franz Hall
> P.O. Box 951563
> Los Angeles, CA 90095-1563
> 
> grisham at lifesci.ucla.edu
> (310) 825-7990
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