[BioC] Query Gene Ontology

[Marc Carlson]

My answer is almost identical to Jims, but I wanted to mention that 
there are also some handy helper functions for the GO mappings such as 
Term() and GOID():

library(org.Hs.eg.db)
library(GO.db)

# here is where I thought that the helper functions might make what we 
are doing bit easier to see?  (YMMV)
goID <- GOID( GOTERM[ Term(GOTERM) == "myelination" ] )

# the rest is going to be basically the same.
get(goID, org.Hs.egGO2ALLEGS)


   Marc



On 05/18/2011 10:40 AM, James W. MacDonald wrote:
> Hi Herve,
>
> On 5/18/2011 9:16 AM, LEMAITRE Hervé Université Paris Sud wrote:
>> Dear bioconductor-users,
>>
>>
>>
>> I'm looking for a way to query the gene ontology in R like in the GO
>> browser (AmiGO). I tried different packages (NCBI2R, GOsim ...) but I
>> did not find a simple way to extract genes names associated to a GO
>> term (i.e. myelination). Could you tell me if there is a way to do
>> that?
>
> > library(org.Hs.eg.db)
> > library(GO.db)
> > ind <- x[x$Term == "myelination",1]
> > ind
> [1] "GO:0042552"
> > egs <- get(ind, org.Hs.egGO2ALLEGS)
> > egs
>     ISS     ISS     IEA     IEA     IEA     IEA     IEA     ISS     
> IEA     NAS
>   "745"   "928"  "1000"  "1959"  "2064"  "3073"  "3074"  "3170"  
> "3611"  "4118"
>     TAS     IEA     IEA     IEA     ISS     IEA     IEA     IEA     
> IEA     IEA
>  "4118"  "4155"  "4664"  "4665"  "4763"  "4908"  "5354"  "5376"  
> "5453"  "5454"
>     NAS     ISS     ISS     IEA     ISS     IEA     IEA     IEA     
> ISS     IEA
>  "5653"  "6326"  "6334"  "6497"  "6647"  "7038"  "7040"  "7248"  
> "7572"  "8443"
>     IMP     IMP     IMP     ISS     IEA     ISS     IEA     IEA     
> ISS     ISS
>  "8890"  "8892"  "8893"  "9451"  "9514"  "9921" "10215" "10939" 
> "11202" "23114"
>     NAS     ISS     IEA     IEA     ISS     NAS     IEA
> "23205" "23405" "50846" "51090" "57463" "81846" "84504"
>
> You could filter at this point, if you wanted e.g., just ISS terms.
>
> > genes <- unlist(mget(egs, org.Hs.egSYMBOL))
> > genes
>       745       928      1000      1959      2064      3073      3074 
>     3170
> "C11orf9"     "CD9"    "CDH2"    "EGR2"   "ERBB2"    "HEXA"    "HEXB" 
> "FOXA2"
>      3611      4118      4118      4155      4664      4665      4763 
>     4908
>     "ILK"     "MAL"     "MAL"     "MBP"    "NAB1"    "NAB2"     "NF1" 
>   "NTF3"
>      5354      5376      5453      5454      5653      6326      6334 
>     6497
>    "PLP1"   "PMP22"  "POU3F1"  "POU3F2"    "KLK6"   "SCN2A"   "SCN8A" 
>    "SKI"
>      6647      7038      7040      7248      7572      8443      8890 
>     8892
>    "SOD1"      "TG"   "TGFB1"    "TSC1"   "ZNF24"   "GNPAT"  "EIF2B4" 
> "EIF2B2"
>      8893      9451      9514      9921     10215     10939     11202 
>    23114
>  "EIF2B5" "EIF2AK3" "GAL3ST1"   "RNF10"   "OLIG2"  "AFG3L2"    "KLK8" 
>  "NFASC"
>     23205     23405     50846     51090     57463     81846     84504
>  "ACSBG1"  "DICER1"     "DHH"    "PLLP"  "AMIGO1"    "SBF2"  "NKX6-2"
>
> Best,
>
> Jim
>
>
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Hervé
>>
>>
>>
>>
>>
>> `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´ 
>>
>>
>>  Hervé Lemaître
>>
>> U1000 "Imagerie et Psychiatrie"
>>
>> INSERM - CEA - Faculté de Médecine Paris Sud 11
>>
>> Service Hospitalier Frédéric Joliot
>>
>> 4, Place du Général Leclerc
>>
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>>
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>>
>> Fax: (+33) 1 69 86 78 10
>>
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>>
>>
>>
>>
>>
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