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 Post subject: Total Gene list
PostPosted: Tue Dec 03, 2013 4:24 am 
How can I get the list of genes in the "Total Genes" column in the "GREAT" results table that associate with a particular ontology? I followed the guidance given in your webpage under "What statistics are given for each ontology listed below?". I downloaded the list of "gene product associations" from the link "GREAT" provides to Amigo and tried to reproduce the number given by the "GREAT" results table but I could not. The numbers are close but not exactly the same.

I need to have this list to be able to repeat the analysis on my local computer using a large background set of over 4 million regions. I want to test if the association of my foreground list is enriched relative to my large background set. To do this, I would like to test the association of this background set with the exact number and identity of genes that are called by the online "GREAT" software but so far the numbers (number of total genes from the GREAT results and those from the downloaded gene product associations) don't match exactly.

Thank you for doing a "great" job by the way.
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PostPosted: Mon Dec 09, 2013 12:08 pm 
Site Admin
Thank you for your question and for using GREAT. We don't routinely provide these gene lists and it sounds like your list should get very similar enrichments and rank order. You can run queries on the website from api if possible.

Best wishes,

The GREAT Team
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