Default data sets for gene expression change?

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Dan Beisner

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Mar 29, 2017, 12:45:32 PM3/29/17
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Hello,

 

Did you guys change the default data sets for gene expression recently?  I am used to the ones that have the immune cells on the bottom in a different color and I don’t see that one in default anymore.  It has a lot more tissue types which is cool, but wanted to double check if this is the way it is moving forward. 

 

Thanks!

Dan

 

 

Dan Beisner

Associate Director, Discover Biology

Vividion Therapeutics

3033 Science Park Rd

San Diego, CA 92121

(858)342-7226

 

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G Tsueng

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Mar 30, 2017, 10:38:58 AM3/30/17
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Hi Dan,

Thanks for using BioGPS and reaching out to us about this issue.  Just to clarify your question, is the default dataset you're accustomed to seeing no longer available in the selection menu (pops up when you click on 'change dataset'), or is it no longer the first one you see?  If it's no longer available in the selection menu when changing datasets, how recently did this happen?  Last week, last month, last year?  The reason I ask is because some default datasets don't appear in the selection list depending on the gene (https://groups.google.com/forum/#!searchin/biogps/default$20dataset|sort:relevance/biogps/lRWVd2cLNB4/D-apKFOQAgAJ ) which is an issue that's been observed since last year, but if you've noticed the change more recently on something you check quite regularly it might be a different issue.  If it's no longer the first one you see (but you are able to select the one you want from the selection list when you click 'change dataset'), its possible that you've landed on one of the multiple default datasets available for that gene.

best wishes,
ginger

Dan Beisner

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Apr 4, 2017, 6:54:12 PM4/4/17
to G Tsueng, BioGPS

Sorry for delayed response, but thanks for the follow up.

 

Checked a couple of other genes and it was the same 2 defaults that pop up (and those were the only 2 default options).  It probably started 2-4 weeks ago. 

 

But I just clicked the link below, and now there are 6 default datasets.  So that’s good. 

 

Dan

Andrew Su

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Apr 4, 2017, 7:56:14 PM4/4/17
to BioGPS, G Tsueng, Dan Beisner
Hi Dan,

I'm pretty sure the issue here is that the gene you queried does not have any data in the standard "Gene Atlas" data set (http://biogps.org/dataset/GSE1133/).  Note that this data set was run on the older "U133A" array.  In that situation, BioGPS tells you that there are only two of the default data sets that do have data for that gene.  When/if you select one of those data sets (eg the "Barcode" dataset shown above), then future gene searches will continue to show that data set even when the Gene Atlas data is available.  Hope that makes sense...

Best,
-andrew

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