Reduce redundancy in a GO enrichment analysis
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Entering edit mode
6.6 years ago
dago ★ 2.7k

I performed a GO enrichment analysis using topGO in BioC.

The analysis worked perfectly and now I get the following GO enriched (GO_ID) with the respective p-values (Fisher):

 

>head(cyt.MF.merged.combined[,c("GO_ID","Fisher")] )

 GO_ID  Fisher
1 GO:0000156 0.01314
2 GO:0004322 0.01705
3 GO:0004519 0.04516
4 GO:0004601 0.01917
5 GO:0005315 0.01705
6 GO:0008509 0.00769    

 

However, many terms (e.g. GO:0016722, GO:0016724) are one the child of the other.

Since I do not need such a level of details, I was wondering if there is a tool to combine those terms that are related in a lower level of annotation. Of course, I would need to recalculate another p-value for the obtained parent node.

Has anyone experience with that?

Thanks in advance.

GO geneenrichment Bioconductor • 3.7k views
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Entering edit mode

Thanks for your answer. I know GOstats, and you are right it is a good tool for this kind of analysis. I was just wondering if is available another tool which can reduce redundancy  after the enrichmetn is already performed with topGO.

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Entering edit mode
6.6 years ago
russhh 5.5k

You could use GOstats, which provided a `conditional=TRUE` argument is provided to hyperGTest, can account for some of the conditional dependencies between GO terms

HTH

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Entering edit mode
6.5 years ago

Have a look at Revigo and/or EnrichmentMap (although revigo seems to be down just now...).

Dario

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