[BioC] comparing GO lists

Robert Gentleman rgentlem at fhcrc.org
Sun Jul 29 01:15:51 CEST 2007

Hi Ana,
   I have cc'd the response to the list,

have a look at the GOstats package (there may be others in other 
packages) it has simUI, simLP that take GO graphs as input. 
Unfortunately they do not use semantic similarity - I don't think that 
there is anything in Bioconductor that does that (but could be wrong).

There was some software (not in R) and a paper by Peter Lord,
Investigating semantic similarity measures across the Gene Ontology: the 
relationship between sequence and annotation.
Lord PW, Stevens RD, Brass A, Goble CA.
in Bioinformatics in 2003 that would be nice to have, but last time I 
looked it was not functional -

best wishes

Ana Conesa wrote:
> Hello Robert,
> For some reason my posting to the Bioconductor list is not working
> today... but I guess you are the most appropirate person for my
> query, so I hope you do not mind I write to you directly.
> Best regards,
> Ana
> Dear list,
> I am looking for a function to compare lists of GO terms, e.g. compute
> semantic similarity or the minimum common graph, etc, that works with
> GO
> ids... I looked into the GO packages at Bioconductor but it seems to
> me
> that functions to perform such comparisons only accept as input list
> of
> gene IDs, and not GO IDs. Am I right/wrong?
> Any help appreciated
> Cheers
> Ana
> ===============================================
> Ana Conesa, PhD
> Bioinformatics Department
> Centro de Investigacion Principe Felipe
> Avda Autopista Saler 16, 46013 Valencia, Spain
> http://bioinfo.cipf.es
> --------------------------------
> CAMDA 2007 Conference at CIPF
> http://camda.bioinfo.cipf.es
> --------------------------------

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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