[Bioperl-l] Clustering of Gene Ontology Terms

Ryan Golhar golharam at umdnj.edu
Thu Feb 21 07:26:58 EST 2008


ArrayTrack is a good tool to do this, available from the FDA.  It has 
some nice output and performs some statistical analysis for you.  I'm 
using it now to cluster GO terms.

Thiago M. Venancio wrote:
> 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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