Calculating GO Term enrichment

Question

[ben.ward]

Hi,

I have a set of transcripts that a collegaue has identified as being up regulated in a study species cf. a reference species. Each transcript has a set of GO terms associated with it. The GO Terms were pulled from a gb file.

The data is in R in a list, names are transcript ID, and the values are the GO terms.

e.g.

$WS010775.1
[1] "0042567" "0005634" "0007155"

$WS007996.2
 [1] "0005834" "0005886" "0003924" "0004871" "0010659" "0071456" "0042462" "0007186" "0007602" "0008104" "0007165" "0007268"

$WS010604.4
[1] "0016021" "0007155"

I'd like to present a summary of biological function/features that are represented by those up regulated transcripts. I found REVIGO (http://revigo.irb.hr/) but I believe that it requires that I do GO Term enrichment first to get the p-values that REVIGO requires. Are there any tools I can use to do this, given that the species I'm study is not human/mouse/etc? Tools I've looked at find the terms and do enrichment analysis. But I already know the GO terms of each transcript, I just want to calculate enrichment.

Thanks,

Ben W.

Answer 1

[Sean Davis]

One of the easiest GO enrichment tests to apply is the Fisher Exact Test approach. Take a look at this response: http://stats.stackexchange.com/a/72556/5143. This is easily done in R.