[BioC] GO's to gene's
Martin Morgan
mtmorgan at fhcrc.org
Mon Mar 1 14:16:48 CET 2010
On 02/28/2010 09:01 PM, Loren Engrav wrote:
> So I checked
>> collagen
> And this list matches Amigo
> So then would appear the issue lies in
>> egids <- mget(names(collagen), org.Hs.egGO2EG, ifnotfound=NA)
> Some of the names are finding no associated genes in org.Hs.egGO2EG and so
> appear as NA
> True? Possible?
yes. GO is not H. sapiens specific and ENTREZ ids are not 100%
comprehensive, so some GO terms do not map to ENTREZ ids.
>>> Also I would like to omit the IEA group
maybe
egids <- lapply(egids, function(elt) elt[names(elt) != "IEA"])
egids[sapply(egids, length) != 0]
Martin
> My version of org.Hs.egGO2EG is 2.3.6
>
>
>
>
>
>> From: Loren Engrav <engrav at u.washington.edu>
>> Date: Sun, 28 Feb 2010 20:33:05 -0800
>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Conversation: [BioC] GO's to gene's
>> Subject: Re: [BioC] GO's to gene's
>>
>> Oopps, Amigo says there are 20 such terms, not 68 as I said before, cuz I
>> retrieved only BP
>>
>>
>>> From: Loren Engrav <engrav at u.washington.edu>
>>> Date: Sun, 28 Feb 2010 20:28:17 -0800
>>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>> Conversation: [BioC] GO's to gene's
>>> Subject: Re: [BioC] GO's to gene's
>>>
>>> Ok thank you
>>> I now show
>>>> sessionInfo()
>>> R version 2.10.1 (2009-12-14)
>>> i386-apple-darwin9.8.0
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] org.Hs.eg.db_2.3.6 GO.db_2.3.5 RSQLite_0.8-3
>>> AnnotationDbi_1.8.1 DBI_0.2-5
>>> [6] Biobase_2.6.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.10.1
>>>
>>> And all commands pass with no errors, however I see
>>>
>>>> egids
>>> $`GO:0010711`
>>> IEP
>>> "1471"
>>>
>>> $`GO:0030199`
>>> IEA IEA ISS IEA IMP IMP IMP IMP NAS
>>> IMP NAS IMP ISS
>>> "302" "304" "538" "871" "1277" "1278" "1280" "1281" "1281"
>>> "1289" "1289" "1290" "1290"
>>> NAS IDA NAS IEA IEA IEA IEA IEA NAS
>>> ISS IDA ISS NAS
>>> "1301" "1302" "1303" "1805" "2296" "2303" "4010" "4015" "4060"
>>> "4763" "7042" "7046" "7373"
>>> NAS NAS
>>> "9508" "50509"
>>>
>>> $`GO:0030574`
>>> IEA IEA IEA IEA IEA IEA IEA IEA
>>> IEA IEA IEA
>>> "4312" "4313" "4314" "4316" "4317" "4318" "4319" "4320"
>>> "4322" "4325" "4327"
>>> IEA IDA IMP NAS IEA NAS IEA IEA
>>> IEA IEA
>>> "5184" "5645" "5645" "5653" "5657" "9508" "9509" "56547"
>>> "64066" "140766"
>>>
>>> $`GO:0032963`
>>> IEA IMP
>>> "3091" "7148"
>>>
>>> $`GO:0032964`
>>> IEA IMP IMP TAS IMP
>>> "871" "1277" "1281" "1281" "1289"
>>>
>>> $`GO:0032966`
>>> IDA IC
>>> "3569" "4261"
>>>
>>> $`GO:0032967`
>>> ISS IDA IDA IC IMP TAS IMP
>>> "265" "2147" "2149" "3066" "7040" "7040" "7043"
>>>
>>> $`GO:0033342`
>>> IMP
>>> "23560"
>>>
>>> So many GO terms containing the word "collagen" are not listed, like
>>> 0004656
>>> 0005518
>>> etc
>>> Amigo claims there are 68 such terms and the list above has only 8
>>> What did I do wrong?
>>> Also I would like to omit the IEA group
>>>
>>> Thank you
>>>
>>>
>>>
>>>
>>>
>>>
>>>> From: Martin Morgan <mtmorgan at fhcrc.org>
>>>> Date: Sun, 28 Feb 2010 19:30:34 -0800
>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>> Subject: Re: [BioC] GO's to gene's
>>>>
>>>> On 02/28/2010 07:17 PM, Loren Engrav wrote:
>>>>> Thank you both
>>>>> Given my skills, it might be easier/quicker to do it "manually" with Amigo
>>>>> But I am trying both methods
>>>>>
>>>>> For the second method I get
>>>>>
>>>>>> library(GO.db)
>>>>> Loading required package: AnnotationDbi
>>>>> Loading required package: Biobase
>>>>>
>>>>> Welcome to Bioconductor
>>>>>
>>>>> Vignettes contain introductory material. To view, type
>>>>> 'openVignette()'. To cite Bioconductor, see
>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>>
>>>>> Loading required package: DBI
>>>>>> terms <- Term(GOTERM)
>>>>> Error in function (classes, fdef, mtable) :
>>>>> unable to find an inherited method for function "Term", for signature
>>>>> "GOTermsAnnDbBimap"
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.9.2 Patched (2009-09-05 r49613)
>>>>> i386-apple-darwin9.8.0
>>>>>
>>>>> locale:
>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>> ,
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> Update to R version 2.10 and associated Bioc packages, or for a (much)
>>>> slower solution (you'll want to check that Term and Ontology return ids
>>>> in identical order)
>>>>
>>>> terms = eapply(GOTERM, Term)
>>>>
>>>> etc. I have
>>>>
>>>>> sessionInfo()
>>>> R version 2.10.1 Patched (2010-02-23 r51168)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] GO.db_2.3.5 RSQLite_0.7-3 DBI_0.2-4
>>>> [4] AnnotationDbi_1.8.1 Biobase_2.6.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.10.1
>>>>
>>>>
>>>> Martin
>>>>
>>>>>
>>>>>> From: Martin Morgan <mtmorgan at fhcrc.org>
>>>>>> Date: Sun, 28 Feb 2010 18:42:33 -0800
>>>>>> To: Vincent Carey <stvjc at channing.harvard.edu>
>>>>>> Cc: Loren Engrav <engrav at u.washington.edu>,
>>>>>> "bioconductor at stat.math.ethz.ch"
>>>>>> <bioconductor at stat.math.ethz.ch>
>>>>>> Subject: Re: [BioC] GO's to gene's
>>>>>>
>>>>>> 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
>>>>>> 1100 Fairview Ave. N.
>>>>>> PO Box 19024 Seattle, WA 98109
>>>>>>
>>>>>> Location: Arnold Building M1 B861
>>>>>> Phone: (206) 667-2793
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>
>>>>
>>>> --
>>>> 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
>
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--
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
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