David enrichment analysis inconsistency
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6.6 years ago
ncl.lazzarini ▴ 120

I have a list of N genes. I used DAVID (http://david.abcc.ncifcrf.gov) in order to get the GO terms that are statistically overrepresented in that list. I selected the GO_BP_FAT subset of terms to not take in account some really generic GO terms (high level terms in the GO tree). Surprisingly I found out something unclear. Given a specific GO term I have a list of genes (defined by DAVID) that should be statistically associated with that term. Now, if I query the Gene Ontology database using the "official" AMIGO interface (http://amigo1.geneontology.org/) I found that the GO term indicated by DAVID is not associated with some genes. For example I found that PAX3, with other genes, is associated with GO:004582, but if you query Amigo you don't get this term. How is this possible?

david enrichment analysis gene ontology • 2.5k views
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As far as I remember, there could be an issue with GO version in DAVID, which was not updated for quite a long time.

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From the website it seems that the last update was on 2009 (5 years ago). I don't know exactly how the association between GO terms and gene works, but this means that some associations might have been deleted across the years right?

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Yep.. deleted, added, changed. The amigo page actually mentions "GO database release 2014-10-18", so you're right about 5 year difference

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if they really did not update for 5 years it would be mind bending

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I would recommend using a different tool, like ermineJ

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When I started doing bioinformatics a year ago, david wasted a lot of my time because of these kind of issues and yet it was mentioned every where as one of the best GEA tools. Gene Ontology Consortium is definitely a better choice.