[BioC] hypergeometric enrichment of GO terms

[Wolfgang Huber]

Hi Axel

I'd recommend to use "gene set enrichment" analysis, as implemented for 
example in Robert Gentleman's Category package.

Chapter 8 of the vignette of the cellHTS package
http://www.bioconductor.org/packages/1.9/bioc/vignettes/cellHTS/inst/doc/cellhts.pdf
gives an example on how to do this on a scored set of genes whose GO 
annotation
is obtained via biomaRt (the full code of the vignette is provided in the
inst/doc directory of that package).

  Best wishes
   Wolfgang

PS: GO is not really a tree, it is a directed graph.


Axel Rasche wrote:
> Hello,
> 
> For a set of marker genes from a longer list of evaluated genes I would 
> like to test the hypergeometrical enrichment of GO terms. Due to the 
> tree structure of GO terms this is a bit intricate. Can anyone point me 
> to useful functions?
> By now I have lists with Ensembl gene identifiers and the GO annotation 
> can be provided using the package biomaRt.
> 
> In the package GOstats I find the function GOhyperG to compare a 
> differentially expressed genes to all the genes on an Affymetrix chip 
> with the hypergeometric distribution. Unfortunately the package GOstats 
> is restricted to microarray datasets.
> 
> Many thanks for your answer in advance,
> Axel Rasche
>