[BioC] GO summary of a list of genes?

Martin Morgan mtmorgan at fhcrc.org
Tue Feb 19 15:40:57 CET 2008

Likely Bioconductor packages are GO.db and the organism-centric
packages like org.Hs.eg.db, which contain 'maps' between various gene
identifiers and GO terms. You might also find that GSEABase provides
useful functions for creating gene sets representing looser concepts
like 'related to breast cancer', perhaps using concepts defined in the
Broad institute data base of gene sets (see ?getBroadSets) or (with
the devel version of GSEABase) OBO-formated collections

You'd likely use R scripts and / or the Category, GOstats, PGSEA or
other packages to more formally assess whether there is meaningful
signal in the represented pathways.


Ron <yzhu5 at wisc.edu> writes:

> Hello, after using statistical testing, we often obtain a list of genes. 
> Could someone tell me what R/Bioconductor packages I can use to figure 
> out what pathways/functions of these genes are in, e.g. a summary saying 
> that 80% genes are related to breast cancer or 20% genes are related to 
> glucose metabolism pathways? I guess these are GO-related packages.
> Thanks. - Ron
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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