High throughput Gene Ontology enrichment API

[ieuanclay]

A bioinformatics question: I have been doing more and more Gene Ontology (GO) work, specifically, I am looking for enriched terms in my various gene sets. I usually go through the web-based programs like DAVID or Babelomics. However, I now need a high-throughput approach, but was disappointed to only find GO::TermFinder on CPAN.

There are plenty of GO handlers available on CPAN, but far fewer analytical tools, and there are many listed on GO.org, but most are web-based... so I wondered if anyone had any experience of doing GO term enrichment on many, many groups of genes?

1. Any particular API I should use?
2. Any particular problems I should look out for?
3. Is there another web-based program I should think about?
4. Is there a downloadable program that might be a good alternate? (i.e. a commandline based one that I can automate usage of?)

Any help or advice much appreciated!

NB: I have also cross-posted a similar question on PerlMonks...

[tfrayner]

Hi,

I'd personally recommend using either the topGO or GOstats packages from Bioconductor. They're both quite amenable to being used in a high-throughput analysis pipeline, although to get the most out of them you'll want to be comfortable in R.

[ieuanclay]

Thanks for the tip, I hadn't been through Bioconductor yet.

[mgogol]

You might also check out GeneAnswers (also in R).