[BioC] Query Gene Ontology

[James W. MacDonald]

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
>
> 91401 ORSAY, FRANCE
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> Tél:  (+33) 1 69 86 77 84
>
> Fax: (+33) 1 69 86 78 10
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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