using the goana function from edgeR
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David Rengel ▴ 70
@david-rengel-6321
Last seen 3 months ago
European Union

Hi, I have what I think are three simple questions regarding the goana() function of edgeR, which I am not very familiar with:

1-Does it work with Arabidopsis?

2- I understand that if the coefficient you are looking into is cond.B - cond.A, you'd be fishing out terms that are differently represented between B and A, if I am right. What if you want to compare GO terms from DE genes in cond.B - cond.A against the GO terms from the whole genome or from all genes in the dataset?

3-If looking into cond.B - cond.A will render terms that are differently represented between B and A, what if you are looking into an interaction-type contrast such as (cond.A1 - cond.B1) - (cond.A0 - cond.B0). What would be the interpretation of goana results?

Thanks a lot for any help you may provide me with on those.

Best,

David

RNASeq edgeR GO GOSemSim • 410 views
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@gordon-smyth
Last seen 2 minutes ago
WEHI, Melbourne, Australia

Does it work with Arabidopsis?

Typing ?goana brings up a help page that lists possible species. The pages refers you to ?alias2Symbol, which gives a comprehensive list. No, Arabidipsis isn't one of them. For more explanation see:

You could however convert the Arabidopsis GO annotation to a data.frame and then use kegga instead of goana to do the same analysis:

I understand that if the coefficient you are looking into is cond.B - cond.A, you'd be fishing out terms that are differently represented between B and A, if I am right.

No, not exactly. goana is looking for terms that a over-represented in the DE genes, not merely associated with the DE genes.

What if you want to compare GO terms from DE genes in cond.B - cond.A against the GO terms from the whole genome or from all genes in the dataset?

That's exactly what is done. That's what we mean by over-representation. See the universe argument.

what if you are looking into an interaction-type contrast such as (cond.A1 - cond.B1) - (cond.A0 - cond.B0). What would be the interpretation of goana results?

goana works the same for any contrast. It looks for GO terms are over-represented amongst the DE genes relative to all annotated genes in the dataset.

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Thanks a lot Gordon,

I misunderstood the way the analysis are performed, I see now it works the way topGO does. It is nice to have annotation analysis function within edgeR. I allow myself to reproduce the phrase in page 26 of the users' guide that might have mislead me. Otherwise is fine, but I wonder if this phrase reflects what it is really done with goana() Thanks again for your help.

Best,

David.

"Suppose we want to identify GO terms and KEGG pathways that are over-represented in group 2 compared to group 1 from the previous example in Section 2.11.3 assuming the samples are collected from mice"

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goana does an over-representation analysis so the User's Guide wording seems correct. If you don't use the extra capabilities of goana to adjust for gene length or other variables, then it is similar to other GO tools as the analysis is very standard.