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I ran an enrichment analysis with custom annotations using TopGO and surprisingly I obtained new GO terms inside the significant GO terms.

Is that possible? The only reason I can imagine this is possible is because TopGO adds new GO terms based on the input GO terms, since GO ontology is structured hierarchically.

Please let me know if you need more details about the experiment.

Code:

https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing

TopGO output:

https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing

Thanks, Bernardo

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  • $\begingroup$ These new GO terms seem to be the parents of the already GO terms present in my original dataset. $\endgroup$ – biotech Oct 29 '13 at 19:17
  • $\begingroup$ You seem to have answered your own question with that comment. Is everything clear now? Do you understand why the parents appear? $\endgroup$ – terdon Oct 30 '13 at 0:15
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These new GO terms seem to be the parents of the already GO terms present in my original dataset.

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Looking over your code I see that you are using the Fisher exact test (FET). Several assumptions of the FET are not meet when testing gene sets by GO annotation (cite). If this is for a school project FET is good enough. However, if this data set is for publication I would recommend using a different analysis. I don't know what your data looks like and the questions your trying to answer, but I would start by looking at these: Review, Camera (Wu 2012), ROAST (Wu 2010), and the first article I linked to.

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