[BioC] Get Gene annotation (GO terms)

[Marc Carlson]

Hi David,

For human you want to use org.Hs.eg.db.

Other packages may also contain GO terms but not mapped onto the correct 
set of genes.  So if instead you had used org.Mm.eg.db, you would find 
GO terms mapped only onto mouse genes and symbols.


   Marc



On 03/17/2011 02:21 PM, David martin wrote:
> Perfect it's human,
> I guess i can then use any of the GO packages to get signficant 
> Goterms. Which one would you suggest ?
>
> On 03/17/2011 10:16 PM, Marc Carlson wrote:
>> What species? Those look like human gene symbosl, so I will give an
>> example for that:
>>
>> library(org.Hs.eg.db)
>> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2")
>> ## Then you can just merge together the GO to entrez gene mappings with
>> the SYMBOL to entrez gene mappings like this:
>> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x=
>> "gene_id", by.y="gene_id")
>>
>> Does that make sense?
>>
>>
>> Marc
>>
>>
>> On 03/17/2011 02:11 PM, David martin wrote:
>>> Hi,
>>> Which package should i use to convert a list of gene names
>>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get
>>> a list of significant GO terms based on the input genes).thanks for
>>> pointing me to right direction.
>>>
>>> thanks,
>>> david
>>>
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>>
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>
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