[Bioperl-l] Clustering of Gene Ontology Terms
Thiago M. Venancio
thiago.venancio at gmail.com
Thu Feb 21 07:00:10 EST 2008
This is off topic, but here we go.
For enrichment analysis, I use Ontologizer:
But I am also not sure what do you mean by clustering.
On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer <shameer at ncbs.res.in> wrote:
> > Dear All,
> > Is there any module available in Bioperl that can be used to perform
> > clustering of Gene Ontology terms from a set of Gene IDs and its
> > respective Flybase GO annotations. These Gene IDs where hits from a
> > high-throughput experiment. We would like to find the GO-Term enriched
> > areas to get better biological insight irrespective of the experimental
> > parameters.
> > I am extremely sorry if this is off-topic :
> > Can you please point me towards any paper/libraries that had used Gene
> > Ontology based clustering ?
> 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. If you are looking for programmatic support for custom
> pipelines, you can look at R/Bioconductor.
> Here is a website that will look for GO enrichment and takes Flybase
> IDs as the gene identifier:
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
"At the center of your being you have the answer; You know who you are and
you know what you want."
Thiago Motta Venancio, M.Sc., PhD
Laboratory of Bioinformatics
University of Sao Paulo
More information about the Bioperl-l