[BioC] From a list of annotated interesting genes to a list of GO's 'interesting' Biological Processes

[Massimo Pinto]

Greetings all,

Using limma's fitting approach and topTable(), I have reached the nice
point of having produced lists of annotated interesting genes.
Graphically, I can now compare across my contrasts using Venn
diagrams, and I can build Volcano plots etc.

As I am  making my early steps into Gene Ontology, I believe that the
audience before which I will present my data will expect me to
highlight which Biological Processes were significantly (and with what
significance) involved in my experiments, and what differences I found
across my contrasts. What solutions are available via Bioconductor to
address these data analysis and reporting questions? Is GOstats useful
in this regard?

My major reference is ' Bioinformatics and computational biology
solutions using R and Bioconductor'. I have tried to use the annaffy
package and aafTableAnn(), with its subsequent html export mode, but
this outputs all three ontologies, whereas I may wish to limit myself
to Biological Processes for the moment. Also, I would prefer to see an
output in which BP GOs are listed with the number of my 'interesting
genes' falling into them. Not sure whether this is a standard way of
reporting these data, but I hope that you may have some simple advice
on this matter.

Thanking you in advance,

Yours,
Massimo P.


Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto