[BioC] Genbank accessions for GOstuff

[James W. MacDonald]

Also note that you can easily map your GenBank IDs to GO IDs or a host 
of other IDs using biomaRt.

Best,

Jim



Sean Davis wrote:
> 
> 
> On 8/9/06 3:02 AM, "adlai burman" <fsajb4 at uaf.edu> wrote:
> 
> 
>>The GO packages seem to rely solely on LocusLink ids but there are a
>>host of onboard affy translators. Now LL seems to be deprecated and I
>>don't use affymetrix.
> 
> 
> Locuslink has simply been replaced by Entrez Gene.  For nearly all intents
> and purposes, Locuslink still exists, but has the name Entrez Gene.  So,
> when you read about Locuslink-based analyses, these are still appropriate
> and possible.  
> 
> 
>>I have thousands of genes which I would love to
>>continue using with BioC. Does anyone know of a mapping somewhere where
>>I can batch convert gb nums or gene symbols in a way that R's GO
>>packages will accept. Thanks in advance.
> 
> 
> The AnnBuilder package is the way to build an annotation package for your
> genes.  It takes genbank ids and makes an annotation package for your array
> that you can then use for downstream analyses.
> 
> Alternatively, there are several online resources that allow you to do GO
> analyses using genbank IDs.  For example, the DAVID/EASE system
> (http://david.niaid.nih.gov/david) supports genbank IDs as input.
> 
> Finally, there are tools to convert your genbank accessions to more useable
> IDs, like Entrez Gene (Locuslink) IDs.  For example, Stanford Source (
> http://source.stanford.edu/cgi-bin/source/sourceSearch) can convert between
> genbank IDs and multiple gene identifiers.
> 
> Sean
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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