[BiO BB] tissue specificity

[Ryan Raaum]

Have you looked at the Novartis SymAtlas?

http://symatlas.gnf.org/SymAtlas/

The published reference is http://www.pnas.org/cgi/content/abstract/012025199v1

-Ryan

On Mon, Feb 25, 2008 at 3:54 PM, Samantha Fox <bioinfosm at gmail.com> wrote:
> Mike,
>
>  I appreciate your response. Well, my objective is to look at expression
>  data, with respect to tissue specificity. I needed specific help in this
>  case, as I am not able to find any help or tools/software to deal with
>  tissue specificity information.
>  I came across this tool GeneMerge (http://genemerge.bioteam.net/), and
>  tissuedb from HUSAR group (
>  http://genome.dkfz-heidelberg.de/menu/tissue_db/index.html) ... but have not
>  yet conquered them.
>
>  Anyone with experience on these or similar tools, do point me to FAQs or
>  other details, when using a group of genes to determine tissue specificity
>  of the group.
>
>  ~S
>  On Mon, Feb 25, 2008 at 2:39 PM, Mike Marchywka <marchywka at hotmail.com>
>  wrote:
>
>
>
>  >
>  > Normally when I post to this list I try to provide some background as I
>  > have no idea where
>  > everyone else is interest-wise. I vaguely remember running into something
>  > related while
>  > researching some other topic and went back to do a quick literature
>  > search. I'm not sure
>  > of your immediate problem or state of knowledge but, from what I can find,
>  > this is generally an open
>  > area. For example, you could try reading stuff like this,
>  >
>  >
>  > http://www.ncbi.nlm.nih.gov/pubmed/18194723?ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
>  >
>  > Clin Lab Med. 2008 Mar;28(1):127-43. Links
>  > Data mining for biomarker development: a review of tissue specificity
>  > analysis.Klee EW.
>  > Division of Experimental Pathology, Department of Laboratory Medicine and
>  > Pathology, Mayo Clinic, 200 1st Street SW, Stabile 2-50, Rochester, MN
>  > 55905, USA
>  >
>  >
>  > I was surprised to find many genes labelled, "tissue specific"
>  >
>  > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term="tissue%20specific"
>  >
>  > and maybe you could look into some of the related publications.
>  >
>  > Do you have a specific thesis, problem, or objective?
>  >
>  >
>  >
>  > Mike Marchywka
>  > 586 Saint James Walk
>  > Marietta GA 30067-7165
>  > 404-788-1216 (C)<- leave message
>  > 989-348-4796 (P)<- emergency only
>  > marchywka at hotmail.com
>  > Note: Hotmail is blocking my mom's entire
>  > ISP claiming it is to reduce spam but probably
>  > to force users to use hotmail. Please DON'T
>  > assume I am ignoring you and try
>  > me on marchywka at yahoo.com if no reply
>  > here. Thanks.
>  >
>  > > Date: Mon, 25 Feb 2008 12:26:28 -0600
>  > > From: bioinfosm at gmail.com
>  > > To: bio_bulletin_board at bioinformatics.org
>  > > Subject: [BiO BB] tissue specificity
>  >  >
>  > > Hi all.
>  > >
>  > > Are there any tools, or prediction software for tissue specificity;
>  > given a
>  > > set of genes... what tissue they are most likely to be, or given a set
>  > of
>  > > expression data and tissues.. integrate it all to determing tissue
>  > specific
>  > > genes!
>  > >
>  > > Thanks ..
>  > >
>  > > ~S
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-- 
Ryan Raaum
Anthropology
Lehman College
The City University of New York
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