[Genome] gene description page (adding scores)

[Amanda Miotto]

Dear Sir/Madam

I am looking to do something similar, in the Gene description page (for
example
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=106826982&o=41743127&t=41743158&g=affyHumanExon&i=2332310&i2=2332310&c=chr1&l=41742834&r=41757167&db=hg18&pix=1000
) is it possible to add the results (scores) on this page for custom
tracks. Or if not, even on our own mirror?

Thank you!

A.Miotto








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Hi Kayla,

Thank you for clarifying! I'm still not entirely clear, however, on the
colouring schema. When you say that black indicates that a gene is neither
over- nor under-expressed, what is used as a reference point? I.e. what is
this being compared to?

Thanks again! The rest of your explanation is very useful as I'm still new
to the Genome Browser!

Best,

Fiona


>
> Dear Fiona,
>
>  From the description of your question it seems like you're looking at
> the Known Genes details page for a gene.   I'd like to point out that we
> also have separate tracks for expression data which you may find useful.
>   If you scroll down in the Genome Browser you'll see a subsection of
> track controls called "Expression and Regulation".  Here you can turn on
> various expression data tracks such as "GNF Atlas2" and "Affy Human
> Exon".  Additionally we have a tool called the "Gene Sorter" which lets
> you sort genes based on various criteria, one being "expression".  That
> said, the color coding can be described as follows:
>
> A gene that is more highly expressed in a tissue is colored red and a
> less expressed gene is shown in green. The values are colored on a
> logarithmic scale. Black indicates that a gene is neither over- nor
> under-expressed in the tissue. Uncolored boxes (white or grey on most
> browsers) represent missing data.
>
> I hope this information is helpful to you.  Please don't hesitate to
> contact us again if your require further assistance.
>
> Kayla Smith
> UCSC Genome Bioinformatics Group
>
>
>
> Fiona Young wrote:
>> Hello,
>>
>> I have a question regarding the information on the UCSC genome browser
>> website.
>>
>> Under the "description and page index" for a gene, I'm confused by the
>> display for the "microarray expression data".
>>
>> The description lists red as "high" and green as "low". What does no
>> colour mean? Should I interpret this to mean that:
>>
>> 1. the "reddest" red is highest, no colour is medium expression, and
the.
>> "greenest" green is lowest?
>> or
>> 2. the "reddest" red is highest, the "greenest" green is lowest, and
>> those
>> with no colour have not been investigated?
>>
>> Thanks in advance for your help in clarifying this. Is there also
>> somewhere I can look for more information on this?.
>>
>> Thanks,
>>
>> Fiona Young
>> UBC MD/PhD student, year II
>> Lab of Dr. Michael Hayden
>> Centre for Molecular Medicine & Therapeutics
>> University of British Columbia
>> Lab: 604-875-3809
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
>>