<p>Hi,</p>

<p>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.</p>

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

<p>e.g.</p>

<pre>
$WS010775.1
[1] &quot;0042567&quot; &quot;0005634&quot; &quot;0007155&quot;

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

$WS010604.4
[1] &quot;0016021&quot; &quot;0007155&quot;</pre>

<p>I&#39;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&#39;m study is not human/mouse/etc? Tools I&#39;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.</p>

<p>Thanks,</p>

<p>Ben W.</p>

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.