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Old 08-23-2010, 02:13 AM   #1
ieuanclay
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Location: Basel, Switzerland

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Default High throughput Gene Ontology enrichment API

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...
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Old 08-23-2010, 02:30 AM   #2
tfrayner
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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.
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Old 08-23-2010, 03:09 AM   #3
ieuanclay
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Thanks for the tip, I hadn't been through Bioconductor yet.
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Old 08-23-2010, 06:23 AM   #4
mgogol
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You might also check out GeneAnswers (also in R).
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