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PostPosted: Tue Oct 15, 2013 5:36 am 
I have a simulated BED file that was set up to have high overlap with GO:0035418 (protein localization to synapse). Of the 396 intervals present in the BED file, 197 overlap with the intervals for that GO term (bedtools intersect).

Link to GIST with my input bed file: https://gist.github.com/anonymous/e2b75032fbb73a723708

However, when I run the GREAT web tool using this bed file as my test regions (whole genome background, hg19), GO:0035418 does not show up in the output. That it might not be significant I could wrap my brain around, but I can't figure out why it wouldn't show up at all. Might it have something to do with the fact that the input intervals are larger than what GREAT would typically expect (i.e. they're set up to simulate large regions, rather than CHiPseq peaks)?

Any help or advice would be appreciated.

Thanks
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PostPosted: Tue Oct 15, 2013 6:49 pm 
Site Admin
Hello,

If you ignore statistical significance under "Global Controls" and increase the number of visible rows under "Biological Process" then this term comes up at rank number 442. It's unclear how you created the regulatory domains for the genes in this GO category for your test using bedTool intersect. However, we are looking to see if there is a discrepancy between the AmiGO annotation for this GO category and GREAT.

Best,
The GREAT team
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PostPosted: Wed Oct 16, 2013 5:59 am 
Thanks so much. I missed the "Ignore Statistical Significance" button, but I see it now, and was able to see the GO in question.

As a followup question, is it possible to to "Ignore Statistical Significance" in batch mode using the web API?
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PostPosted: Wed Nov 13, 2013 11:13 am 
Site Admin
Dear User,

It is currently not possible to "Ignore Statistical Significance" in batch mode using the web API. We will consider implementing this in future updates. Thank you for using GREAT.

Best,
The GREAT team
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