[BioC] GO's to gene's

[Martin Morgan]

On 02/28/2010 06:14 PM, Vincent Carey wrote:
> Perhaps there is a package with such functionality.  However, with the
> GO.db package in place, you need to do a little
> programming, perhaps along the lines of
> 
> querGO = function(str, attr = "definition", ont = "MF") {
>   require(GO.db, quietly = TRUE)
>   gc = GO_dbconn()
>   quer.1 = paste("select go_id, term from go_term where",
>   attr, "like('%")
>   quer.2 = "%') and ontology = '"
>   quer.3 = "'"
>   quer = paste(quer.1, str, quer.2, ont, quer.3, collapse = "",
>   sep = "")
>   dbGetQuery(gc, quer)
> }
> 
> whereby
> 
>> querGO("collagen", "term")
>        go_id                                                           term
> 1 GO:0004656                     procollagen-proline 4-dioxygenase activity
> 2 GO:0005518                                               collagen binding
> 3 GO:0008475                      procollagen-lysine 5-dioxygenase activity
> 4 GO:0019797                     procollagen-proline 3-dioxygenase activity
> 5 GO:0019798                       procollagen-proline dioxygenase activity
> 6 GO:0033823                       procollagen glucosyltransferase activity
> 7 GO:0042329 structural constituent of collagen and cuticulin-based cuticle
> 8 GO:0050211                     procollagen galactosyltransferase activity
> 9 GO:0070052                                             collagen V binding
>>

Also

  library(GO.db)
  terms <- Term(GOTERM)  # or maybe Definition(GOTERM) ?
  ontologies <- Ontology(GOTERM)
  collagen <- terms[grepl("collagen", terms) & ("MF" == ontologies)]

and the next step,

  library(org.Hs.eg.db)
  egids <- mget(names(collagen), org.Hs.egGO2EG, ifnotfound=NA)
  egids <- egids[!is.na(egids)]


> 
> On Sun, Feb 28, 2010 at 8:56 PM, Loren Engrav <engrav at u.washington.edu> wrote:
>> Is there a BioC package that will find all the GO terms containing some
>> word, like perhaps ³collagen²
>> And then find all the genes contained within those found terms
>>
>> I scanned
>> GoProfiles
>> GOSemSim
>> GOstats
>> GoTools and
>> TopGO
>>
>> And could not determine that any would do that.
>>
>> Thank you.
>>
>>
>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
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> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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