[BiO BB] proteins related to a particular disease/condition
marchywka at hotmail.com
Wed Mar 10 16:59:20 EST 2010
I think one of the pubmed DB's is something about expression array submissions in computer
readable form. That would probably be your best bet for data compilation.
I guess you could also take empirical observations and chase them through pathway
DB;s for logical consequences ( if A goes up then B must go up etc).
I don't think you will find a numerically accurate cell diagram with an oxygen sensor
and connections therefrom LOL.
Let me know what you do find however as I'm working on some forums for
letting people collate fuzzy stuff like this. When I say fuzzy, "hypoxia" per
se is not a complete environmental or state specification and "your mileage may vary" depending
on the other state variables of the cell.
I do a lot of this kind of thing with barely structured documents. I just got done
trying to pull out peptide sequences from abstracts based on regular
expressions. Still not sure how well I did but I guess you could download all the abstracts
that mention hypoxia and regulation and then remove common words and see what you have
left. Run the uncommon words against the pubmed protein DB and if they come up you
probably have a protein name that has some relevance to your serch criteria.
> Date: Wed, 10 Mar 2010 11:47:39 -0800
> From: drjohn08318 at yahoo.com
> To: bbb at bioinformatics.org
> CC: bbb at bioinformatics.org
> Subject: Re: [BiO BB] proteins related to a particular disease/condition
> Hi Pankaj:
> I doubt this information has been compiled into a neat little table or list. You will probably have to do a Pubmed search and bring together these data from multiple sources. Also, if you go to www.NCBI.nlm.NIH.gov, select "protein" from the pull-down menu, and search for "hypoxia", you will find a list if proteins shown to be modulated by hypoxia.
> John G. Hoey, Ph.D.
> Sent from my iPhone
> On Mar 9, 2010, at 1:34, Pankaj Khurana wrote:
> Hi all,
> I would like to get a list of all proteins that are
> upregulated/downregulated during hypoxia.
> How can I get a list of these proteins?
> Thanking all in advance
> Dr. Pankaj Khurana
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