[BioC] Genes annotated to GO:0031281 using org.Hs.eg.db
James W. MacDonald
jmacdon at uw.edu
Thu Mar 20 15:38:00 CET 2014
Hi Tim,
Note that you _always_ use a set of genes for hyperGTest. Even if you
started with an array, you can only count a significantly differentially
expressed gene once.
The difference here is that you used the org.Hs.eg.db package as the
annotation rather than some array annotation package, so
probeSetSummary() won't work, as it is trying to match things back to
probe IDs.
So you can do something like this:
gn2go <- select(org.Hs.eg.db, geneIds(hgOverGO), "GOALL")
gos <- summary(hgOverGO)[,1]
golst <- lapply(gos, function(x) gn2go[gn2go[,2] %in% x,])
Best,
Jim
On 3/19/2014 7:03 PM, Tim Smith wrote:
> Hi James,
>
> Hmmm....I seem to get an error if I use probeSetSummary. As I
> mentioned before I run the hyperGTest using a set of genes (and not a
> set of probes).
>
> Here is what I get:
>
> hgOverGO <- hyperGTest(paramsGO)
>
> > hgOverGO
> Gene to GO BP Conditional test for over-representation
> 3843 GO BP ids tested (220 have p < 0.05)
> Selected gene set size: 318
> Gene universe size: 6088
> Annotation package: org.Hs.eg
>
> > class(hgOverGO)
> [1] "GOHyperGResult"
> attr(,"package")
> [1] "GOstats"
>
> > head(summary(hgOverGO))
> GOBPID Pvalue OddsRatio ExpCount Count Size Term
> 1 GO:0007268 2.658284e-07 2.645556 19.0653745 43 365
> synaptic transmission
> 2 GO:0001975 1.299252e-06 21.622722 0.6790407 7 13 response
> to amphetamine
> 3 GO:0035637 2.726576e-06 2.320191 22.8784494 46 438
> multicellular organismal signaling
> 4 GO:0072511 1.195032e-05 3.566708 6.2680683 19 120
> divalent inorganic cation transport
> 5 GO:0018958 1.788607e-05 9.280645 1.2536137 8 24
> phenol-containing compound metabolic process
> 6 GO:0042886 2.537415e-04 3.066360 5.9546649 16 114
> amide transport
>
>
> > ps <- probeSetSummary(hgOverGO,pvalue=0.05)
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function ‘columns’ for
> signature ‘"function"’
>
> > traceback()
> 7: stop(gettextf("unable to find an inherited method for function %s
> for signature %s",
> sQuote(fdef at generic), sQuote(cnames)), domain = NA)
> 6: (function (classes, fdef, mtable)
> {
> methods <- .findInheritedMethods(classes, fdef, mtable)
> if (length(methods) == 1L)
> return(methods[[1L]])
> else if (length(methods) == 0L) {
> cnames <- paste0("\"", sapply(classes, as.character),
> "\"", collapse = ", ")
> stop(gettextf("unable to find an inherited method for function %s for
> signature %s",
> sQuote(fdef at generic), sQuote(cnames)), domain = NA)
> }
> else stop("Internal error in finding inherited methods; didn't
> return a unique method",
> domain = NA)
> })(list("function"), function (x)
> standardGeneric("columns"), <environment>)
> 5: columns(db)
> 4: match(x, table, nomatch = 0L)
> 3: map %in% columns(db)
> 2: getAnnMap(ids, annotation(result))
> 1: probeSetSummary(hgOverGO, pvalue = 0.05)
>
>
> Am I calling the probeSetSummary function incorrectly?
>
>
> thanks!!
>
>
> On Wednesday, March 19, 2014 5:54 PM, Tim Smith
> <tim_smith_666 at yahoo.com> wrote:
> Hi James,
>
> Thanks for the reply! I had 371 genes ( gene universe ~ 7k genes) for
> which I was checking enrichment and I got this term as one of the
> significant terms. The details are:
>
> GOBPID Pvalue OddsRatio ExpCount Count Size
> Term
> GO:0031281 0.021301601 10.113271 0.22913929 2 15
> positive regulation of cyclase activity
>
> I used GOstats for this analysis. If Count = 2, then shouldn't there
> be two genes that are directly annotated to this term?
>
>
>
>
>
> On Wednesday, March 19, 2014 10:17 AM, James W. MacDonald
> <jmacdon at uw.edu <mailto:jmacdon at uw.edu>> wrote:
>
> Hi Tim,
>
> There may not be any IDs mapped to that term directly. You can use
> GO2ALLEGS, which maps all direct and child terms to Entrez Gene IDs.
>
> > get("GO:0031281", org.Hs.egGO2ALLEGS)
> IDA IDA TAS TAS IDA TAS IEA TAS TAS
> TAS
> "49" "116" "116" "117" "135" "135" "136" "136" "140"
> "153"
> IDA IDA TAS IDA IEA IDA IDA TAS IDA
> IEA
> "154" "155" "554" "796" "796" "799" "1394" "1394" "1812"
> "1812"
> IDA IEA NAS TAS TAS IEA TAS TAS IEA
> TAS
> "1816" "1816" "1816" "1816" "1909" "2692" "2696" "2740" "2774"
> "2778"
> IDA ISS ISS IBA IBA IMP ISS TAS TAS
> TAS
> "2852" "3973" "4763" "4842" "4843" "4846" "4846" "4914" "4915"
> "5032"
> ISS NAS IEA IDA IEA TAS TAS
> "5578" "5894" "7077" "7432" "7434" "10486" "10487"
>
> Or the more powerful select() method:
>
> > select(org.Hs.eg.db, "GO:0031281", c("ENTREZID", "SYMBOL"), "GOALL")
> GOALL EVIDENCEALL ONTOLOGYALL ENTREZID SYMBOL
> 1 GO:0031281 IDA BP 49 ACR
> 2 GO:0031281 IDA BP 116 ADCYAP1
> 3 GO:0031281 TAS BP 116 ADCYAP1
> 4 GO:0031281 TAS BP 117 ADCYAP1R1
> 5 GO:0031281 IDA BP 135 ADORA2A
> 6 GO:0031281 TAS BP 135 ADORA2A
> 7 GO:0031281 IEA BP 136 ADORA2B
> 8 GO:0031281 TAS BP 136 ADORA2B
> 9 GO:0031281 TAS BP 140 ADORA3
> 10 GO:0031281 TAS BP 153 ADRB1
> 11 GO:0031281 IDA BP 154 ADRB2
> 12 GO:0031281 IDA BP 155 ADRB3
> 13 GO:0031281 TAS BP 554 AVPR2
> 14 GO:0031281 IDA BP 796 CALCA
> 15 GO:0031281 IEA BP 796 CALCA
> 16 GO:0031281 IDA BP 799 CALCR
> 17 GO:0031281 IDA BP 1394 CRHR1
> 18 GO:0031281 TAS BP 1394 CRHR1
> 19 GO:0031281 IDA BP 1812 DRD1
> 20 GO:0031281 IEA BP 1812 DRD1
> 21 GO:0031281 IDA BP 1816 DRD5
> 22 GO:0031281 IEA BP 1816 DRD5
> 23 GO:0031281 NAS BP 1816 DRD5
> 24 GO:0031281 TAS BP 1816 DRD5
> 25 GO:0031281 TAS BP 1909 EDNRA
> 26 GO:0031281 IEA BP 2692 GHRHR
> 27 GO:0031281 TAS BP 2696 GIPR
> 28 GO:0031281 TAS BP 2740 GLP1R
> 29 GO:0031281 IEA BP 2774 GNAL
> 30 GO:0031281 TAS BP 2778 GNAS
> 31 GO:0031281 IDA BP 2852 GPER1
> 32 GO:0031281 ISS BP 3973 LHCGR
> 33 GO:0031281 ISS BP 4763 NF1
> 34 GO:0031281 IBA BP 4842 NOS1
> 35 GO:0031281 IBA BP 4843 NOS2
> 36 GO:0031281 IMP BP 4846 NOS3
> 37 GO:0031281 ISS BP 4846 NOS3
> 38 GO:0031281 TAS BP 4914 NTRK1
> 39 GO:0031281 TAS BP 4915 NTRK2
> 40 GO:0031281 TAS BP 5032 P2RY11
> 41 GO:0031281 ISS BP 5578 PRKCA
> 42 GO:0031281 NAS BP 5894 RAF1
> 43 GO:0031281 IEA BP 7077 TIMP2
> 44 GO:0031281 IDA BP 7432 VIP
> 45 GO:0031281 IEA BP 7434 VIPR2
> 46 GO:0031281 TAS BP 10486 CAP2
> 47 GO:0031281 TAS BP 10487 CAP1
> Warning message:
> In .generateExtraRows(tab, keys, jointype) :
> 'select' resulted in 1:many mapping between keys and return rows
>
> Best,
>
> Jim
>
>
>
> On 3/19/2014 4:28 AM, Tim Smith wrote:
> > Hi,
> >
> > I was trying to get the genes annotated to the GO term "GO:0031281".
> My code:
> >
> > library(org.Hs.eg.db)
> >
> > genes <- get("GO:0031281", org.Hs.egGO2EG)
> >
> > When I run the code, I get:
> >
> >> genes <- get("GO:0031281", org.Hs.egGO2EG)
> > Error in .checkKeys(value, Rkeys(x), x at ifnotfound
> <mailto:x at ifnotfound>) :
> > value for "GO:0031281" not found
> >
> > If I check in AMIGO for this GO term, it seems to have many gene
> products for Homo sapiens. Am I doing something wrong? Is there an
> alternate package that I can try, just to double check the results?
> >
> > thanks!
> > [[alternative HTML version deleted]]
> >
> >
> >
> > _______________________________________________
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
> [[alternative HTML version deleted]]
>
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>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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