[Bioperl-l] Clustering of Gene Ontology Terms

Thiago M. Venancio thiago.venancio at gmail.com
Thu Feb 21 07:00:10 EST 2008


Hi,
This is off topic, but here we go.
For enrichment analysis, I use Ontologizer:

http://www.charite.de/ch/medgen/ontologizer/

But I am also not sure what do you mean by clustering.

Best.

T

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:
>
> http://niaid.abcc.ncifcrf.gov/home.jsp
>
> Sean
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>



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"At the center of your being you have the answer; You know who you are and
you know what you want."
Lao Tzu

========================
Thiago Motta Venancio, M.Sc., PhD
Laboratory of Bioinformatics
University of Sao Paulo
========================


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