RE: GNF data in biomart

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Andrew Su

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May 9, 2011, 9:01:03 PM5/9/11

to Ruth Bar Shir, bio...@googlegroups.com, BioGPS

Hi Ruth,

Interesting question. I wasn’t even aware of that expression filter in BioMart relating back to our data. Unfortunately, I don’t have a good answer for you. We just released and published the raw Gene Atlas data, and it must have been some criterion that the biomart team set to translate that data to a binary expressed / not-expressed call. I’d suggest asking at mart...@ebi.ac.uk.

If you find the answer and let us know here, we’ll send you a BioGPS mascot! (http://biogps.blogspot.com/2008/12/biogps-swag-just-in-time-for-holidays.html)

Cheers,

-andrew

From: Ruth Bar Shir [mailto:bars...@bgu.ac.il]
Sent: Wednesday, May 04, 2011 2:31 AM
To: Ruth Bar Shir
Cc: bio...@googlegroups.com; BioGPS
Subject: GNF data in biomart

Hi,
I have a question regarding the GNF data found in Ensembl
Biomart, since Biomart claims the data is supplied by you.

In the Expression section you can query for genes expressed by a
specific GNF cell type or organism part. I'm working the the
gnf1h-gcrma file and wanted to know which are the threshold you

use in order to consider a gene as expressed in a specific
tissue as given in Biomart.
Thanks,
Ruth‎