[BioC] GO's to gene's
Martin Morgan
mtmorgan at fhcrc.org
Mon Mar 1 03:42:33 CET 2010
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]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
More information about the Bioconductor
mailing list