[Genome] housekeeping genes and tissue specific genes

[Brooke Rhead]

Hello Maria and Frans,

I agree with Frans that there is not a straightforward answer to this 
question.  The genes in the UCSC database are not organized into 
categories like "housekeeping" or "tissue-specific".  However, I could 
make a couple of suggestions about how to proceed.

1) If you have lists of such genes from another source, you can create a 
custom track of the genes and then proceed as previously described to 
generate a custom track of the promoters of those genes:
http://www.soe.ucsc.edu/pipermail/genome/2008-February/015557.html

Information on creating a custom track is here: 
http://genome.ucsc.edu/goldenPath/help/customTrack.html

2) If you know of some Gene Ontology terms 
(http://www.geneontology.org/) that describe the genes of interest, you 
can use the Gene Sorter (http://genome.ucsc.edu/cgi-bin/hgNear) "filter" 
button to find genes that have been assigned those terms.  Additionally, 
you can sort on the Gene Ontology terms to find similar genes.

3) You could start from a known Housekeeping gene or tissue-specific 
gene, and then sort the genes according to gene expression to find 
similar genes.  (Note: I have no idea how reliable this would be.)

Good luck with your research.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Frans Schuit wrote:
> Hi there!
> Interesting question and I am curious for the answer from the UCSC staff
> too.
> 
> However, there may not be a simple answer.  First, the distinction between
> housekeepers and tissue specific genes is not that clear-cut: some
> housekeepers exhibit enormous differences between tissues and some "tissue
> specific ones" are in fact restricted to a series of tissues, e.g.
> neuroendocrine genes.  Second, true cell specific genes can be misclassified
> as "housekeepers" in when evidence is taken from mRNA or protein expression
> in a panel of whole tissues; this is because the specialised cell, e.g. a
> fibroblast, red blood cell, or endothelial cell is present in all tissues.
> 
> Best regards,
> Frans Schuit
> 
> Frans Schuit, MD, PhD
> Gene Expression Unit, Dept. of Molecular Cell Biology
> & K.U. Leuven Center of Excellence in Systems Biology (SymBioSys)
> Katholieke Universiteit Leuven
> Herestraat 49, mailbox 901
> B-3000 Leuven, Belgium
> phone  +32-16-347227
> fax      +32-16-345995
> e-mail:  frans.schuit at med.kuleuven.be
> 
>  
> 
> -----Original Message-----
> From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu] On
> Behalf Of Maria Astrom
> Sent: woensdag 13 februari 2008 9:50
> To: genome at soe.ucsc.edu
> Subject: [Genome] housekeeping genes and tissue specific genes
> 
> Hi there !
>  
> I want to download the coordinates of promoter regions, with categories-
> the HK genes and tissue-specific genes separately.
> Which track I should use for that ?
>  
> Thanks
> Sincerely,
> Maria
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