Querying for overexpression in certain tissues

[Burgess-He...@epamail.epa.gov]

Hi,

I used to use the GNF SymAtlas database to query what genes were highly
expressed in certain tissues. For example, it was possible to download
all genes expressed at 3x the median or greater in the liver, etc. I
cannot see a way to do this in your current format -- is there a way?
And if not, would it be possible to add this functionality back in?

Thank you.

Sincerely,
Sarah Burgess-Herbert
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Sarah Burgess-Herbert, Ph.D.
AAAS Science & Technology Policy Fellow
National Center for Environmental Assessment
Office of Research and Development (8623-P)
U.S. Environmental Protection Agency
1200 Pennsylvania Avenue, NW
Washington, DC 20460

p: 703-347-8979 | f: 703-347-8692
burgess-he...@epa.gov

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[Andrew Su]

Hi Sarah,

Two notes that are relevant to your question.

First, sincerest apologies for the fact that SymAtlas is currently down. It's an unplanned outage, perhaps due to failure of some very old hardware. We've made no secret of our intention to retire SymAtlas, but we were planning on doing it after all the major functionality was available in BioGPS. We're working on trying to get it back up, but it's not looking promising at the moment.

Second, the last major feature to be migrated was some way to search based on expression pattern. SymAtlas had two such features -- "search by expression" (the one you mention below), and "search by correlation". Based on usage we decided to only migrate "search by correlation", which means in the new system, you will have to find a "seed" probe set with the expression pattern you're interested in. The good news is that release of this feature is imminent -- you should see this in BioGPS in the very near future. Keep an eye on the blog for the official announcement...

Hope this helps...

Cheers,
-andrew

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[Andrew Su]

Hi Sarah,

One quick follow up. We kicked the SymAtlas server a little bit harder and it came back online. Users who follow deep links to SymAtlas are now again able to reach specific gene pages (though we'll still try to convince you to go to BioGPS instead). As before, users who try to directly access http://symatlas.gnf.org are still automatically redirected to BioGPS.