Human chromosome proteome mapping?

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Kambiz
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Joined: Tue Nov 29, 2011 12:34 am

Human chromosome proteome mapping?

Postby Kambiz » Tue Apr 17, 2012 9:40 pm

Hi All
Can anybody tell me if it is a good idea that HUPO have started proteome mapping of humans, chromosome by chromosome? Will it work?
Some pepole say it is not a good idea. What are the pros and cons of this approach?
For example, Iran wants to map Y chromosome proteome. In a recently published paper (PMID: 22278370) they were able to identify 4 genes from Y chromosome out of 11731 proteins! As far as I know on the NCBI there are ~429 genes http://www.ncbi.nlm.nih.gov/projects/mapview/maps.cgi?taxid=9606&chr=Y on the Y chromosome and only ~48 proteins http://www.uniprot.org/docs/humchry are seen from Y chromosomse according to Expasy website. What proteomics approaches can be use for proteome chromosome mapping?
Kambiz Gilany, Ph.D.
Assistant Professor
Avicenna Research Institute (ARI)

Evin, Tehran, Iran
P.O. Box: 19615-1177

Tel: +98-21-22432020 Ext. 427
Fax: +98 21 22432021

Website: http://www.avicenna.ac.ir/index.php/en

gadsouza
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Postby gadsouza » Wed Apr 18, 2012 3:20 am

Kambiz wrote: In a recently published paper (PMID: 22278370) they were able to identify 4 genes from Y chromosome out of 11731 proteins!


That is not necessarily surprising, I would bet most of the cell lines using in that paper could be derived from primary cancers in female donors (except for the prostate cancer cell line, for obvious reasons). So if the sampling is over-represented by cells from females, will be harder to identify proteins expressed in the Y chromosome.

I would also think that most of genes in Y are probably expressed in only specific time periods in an individual life, and probably just a few are constitutively expressed. That probably make things harder for the protein miners out there.


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