[BioC] GO's to gene's
Loren Engrav
engrav at u.washington.edu
Tue Mar 2 03:34:54 CET 2010
Thank you
You are clearly very good at this
So to check it all out I did it manually on Amigo. Amigo found 33 genes
(limited to Human and omitting IEA)
The org.HS.eg.db method found 29 of the 33 but did not find
CST3 (1471) GO:0010711 IEP
HIF1A (3091) GO:0032963 ISS
IL6R (3570), GO:0032966 IDA and
TRAM2 (9697) GO:0032964 IMP
I suppose to figure out, for example, why org.Hs.eg.db does not map 9697 to
GO:0032964 is complex
Thank you
> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Mon, 01 Mar 2010 05:16:48 -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 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]]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioconductor mailing list
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>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>> Search the archives:
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>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>
>> _______________________________________________
>> 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
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