[Annotation] mapping genes to GO slims

[Rama Balakrishnan]

1) With AmiGO, you can upload your GAF file in the first step- Input  
your gene product list. You have to click on the pull down and select  
gene association file.

AmiGO doesn't allow you to define your background set, but you can  
define your GO slim terms in the second half.


2) the version at Princeton allows you to define your background set  
also in the Advanced options section.
http://go.princeton.edu/cgi-bin/GOTermMapper

Please let me know if you have any questions.

Rama



On Mar 17, 2009, at 11:37 AM, Doug Howe wrote:

> Perhaps the most repeated question on the lists:
> Does anyone have a bead on the current best way to map a list of  
> genes (symbols or MOD IDs) to a GO slim, with the ability to include  
> and exclude IEA annotations?
>
> AmiGO has some of this, but it isn't clear to me how/if I could  
> provide the ZFIN GAF file along with a list of target genes of  
> interest so the IEAs would be included in the analysis?
>
> Any recommendations?
>
> -Doug
>
> Doug Howe, Ph.D.
> Scientific Curator
> Zebrafish Nomenclature Coordinator
> Zebrafish Information Network
> 541-346-0120
> dhowe at zfin.org
>
>
>
>
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