[Annotation] mapping genes to GO slims

[Doug Howe]

Thanks for the input....here's what our user had to say:

"Thank you so much for all of your help with my problem.  The  
Princeton GO site was perfect and has really accelerated my progress."

Job well done.

-Doug

Doug Howe, Ph.D.
Scientific Curator
Zebrafish Nomenclature Coordinator
Zebrafish Information Network
541-346-0120
dhowe at zfin.org




On Mar 18, 2009, at 10:17 AM, Rama Balakrishnan wrote:

> 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
>>
>>
>>
>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation