[Bioperl-l] Clustering of Gene Ontology Terms

K. Shameer shameer at ncbs.res.in
Thu Feb 21 07:29:01 EST 2008


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 of
> Gene IDs.

In simple terms I have a list of genes, irrespective of any experimental
value I need to cluster them based on their GO-Terms using the Di Acyclic
Graph data structure of the Gene ontology databases.

I found an interesting package from CPAN : GO::TermFinder .
http://search.cpan.org/dist/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 not
part of Bioperl project, I may need to write to the authors.

> 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 :) !!!

>
> Here is a website that will look for GO enrichment and takes Flybase
> IDs as the gene identifier:
> http://niaid.abcc.ncifcrf.gov/home.jsp

Thanks for the link. But I am specifically for something stand alone due
to huge volume of my dataset.

Cheers,
Shameer
NCBS - TIFR



More information about the Bioperl-l mailing list