[Bioperl-l] Clustering of Gene Ontology Terms
cjfields at uiuc.edu
Thu Feb 21 09:21:14 EST 2008
On Feb 21, 2008, at 6:29 AM, K. Shameer wrote:
> Dear All,
> Thanks for your reply.
>> I'm not sure what you mean by GO clustering. However, there are a
>> number of packages that will look for enriched GO terms given a set
>> Gene IDs.
> In simple terms I have a list of genes, irrespective of any
> value I need to cluster them based on their GO-Terms using the Di
> Graph data structure of the Gene ontology databases.
> I found an interesting package from CPAN : GO::TermFinder .
> I am not sure if this is a part of Bioperl :). I have tried with few
> examples it is working fine but I got few wrong results. If this is
> part of Bioperl project, I may need to write to the authors.
It's not part of BioPerl, so you should contact the author.
>> If you are looking for programmatic support for custom
>> pipelines, you can look at R/Bioconductor.
> Thanks a lot !! I have seen a couple of R packages related to GO.
> But, I
> honestly wanted to do it in Perl :) !!!
BioPerl's ontology classes are all in Bio::Ontology and
Bio::OntologyIO. I would also recommend looking at Chris Mungall's go-
>> Here is a website that will look for GO enrichment and takes Flybase
>> IDs as the gene identifier:
> Thanks for the link. But I am specifically for something stand alone
> to huge volume of my dataset.
> NCBS - TIFR
It's always faster to do it locally, I agree, as long as the tools are
available to do so.
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