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Quantifying Specificity of GO Terms
pshannon at systemsbiology.org
Tue Apr 17 21:36:23 PDT 2007
The Bioconductor project has, I believe, a fine solution to this problem -- though
please forgive me if I have misconstrued things. The relevant packages (see
below) use the Hypergeometric distribution to calculate a p-value for the
enrichment of any GO node for the genes in question. I typically map proteins
to GeneID's as the first step in my analysis.
If this sounds like it addresses your problem, you may wish to take a look at
Each of these web pages contains a 'vignette' in a pdf file which makes for
a good introduction to the methods.
Though orginally conceived in the context of microarrays, I use these packages
quite fruitfully with proteomics data.
> > I am working on a project that involves curation of protein data that
> > includes GO terms, and it would be very helpful if I had some
> > numerical quantification of the specificity of each term. It is
> > possible to manually examine each term to determine this specificity,
> > but because there is a large amount of data, I would like to automate
> > the process. I understand that there is no reliable way to do this
> > simply using the level in the DAG hierarchy, but I am wondering if any
> > of you might have a work-around.
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