[BioC] disagreement between biomaRt and topGO
Steffen
sdurinck at lbl.gov
Sat Sep 8 01:04:39 CEST 2007
Hi Dick,
I looked a bit more in detail into the disagreement and it seems like
the biomaRt and GO packages map largely the same entrezgene ids to your
GO term (GO:0006836).
Here's what I did:
I used the GO package to find the entrezgene ids that map to GO:0006836,
I get about 138 unique entrezgene ids using the commands:
library(GO)
entrez = unique(get("GO:0006836",GOENTREZID)).
It looks like these entrezgene ids are a mix of entrezgene ids from all
species.
Of these 138 entrezgene ids, 31 match to the output of our getBM query
in human, which was:
mart=useMart("ensembl",dataset="hsapiens_gene_ensembl")
ids = getBM(c("entrezgene","go"), filters=c("go","with_entrezgene"),
values=list("GO:0006836",TRUE), mart = mart)
The getBM query gave 32 unique entrezgene identifiers.
The only entrezgene id that we found with getBM and that was not found
with the GO package is: 594855
In Ensembl this identifier maps to the uniprot accession Q8WVH0 and the
quickgo search at http://www.ebi.ac.uk/ego/
associated the GO:0006836 id with Q8WVH0. Thus the GO mapping in
Ensembl is correct. Probably this discrepancy is caused by a version
difference between the mappings in the GO package and Ensembl.
I'm not sure how topGO uses the GO package, is it possible there is a
problem in topGO that causes only 11 of these 30+ entrezgene ids to
appear in your analysis? Or did your analysis in topGO filtered out some
of the entrezgene ids? I haven't used topGO before so I'm not sure how
to interpret the example analysis you showed.
> sessionInfo()
R version 2.5.1 (2007-06-27)
i386-apple-darwin8.9.1
locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils"
"datasets" "methods" "base"
other attached packages:
biomaRt RCurl XML GO geneplotter
lattice annotate Biobase RMySQL
"1.11.6" "0.8-0" "1.9-0" "1.16.0" "1.14.0"
"0.15-11" "1.14.1" "1.14.1" "0.6-0"
DBI
"0.2-3"
Cheers,
Steffen
Dick Beyer wrote:
> Hello,
>
> I have a puzzling problem with a disagreement between the numbers of EntrezGene IDs I get from biomaRt and what I get from topGO for the GO category GO:0006836, neurotransmitter transport. I would assume the mismatch would be due to different GO builds, but what I find seems too extreme for that.
>
> Let me give a little background to how I get my list of Entrez Gene IDs.
>
> I start with the file ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz
>
> from which I extract IPI, EG, Symbol, description, UniGene
>
> This eventually gives me a list of 22963 unique Entrez Gene IDs. I process this list through biomaRt as follows:
>
> library(biomaRt)
> mart <- useMart( "ensembl", dataset="hsapiens_gene_ensembl")
> get.go.biomart <-
> getGO(id=ipi.LL.sym.descrip.ug.unique_eg[,2],type="entrezgene",mart=mart)
>
> >From this data.frame I can determine that there are 32 unique Entrez Gene IDs in the Gene Ontology Biological Process category GO:0006836, neurotransmitter transport. Everything is fine so far.
>
> Now I set up things for a topGO (non-affy) calculation:
>
> gene2GO <- as.list(get.go.biomart$go)
> names(gene2GO) <- get.go.biomart$entrezgene
>
> geneList <- list()
> geneList[1] <- list(factor(as.integer(ipi.LL.sym.descrip.ug.unique_eg[,2] %in% LL1027[,2])))
> names(geneList[[1]]) <- ipi.LL.sym.descrip.ug.unique_eg[,2]
>
> This geneList[[1]] has, among its 22963 entries, 32 entries (that is, 32 of the "names" are Entrez Gene IDs) that are in category GO:0006836, and 4 of entries I have marked as significant by setting their values to 1.
>
> Next, I create a topGOdata Biological Process object:
>
> BP.GOdata <- list()
> BP.GOdata[1i] <- list(new("topGOdata", ontology = "BP", allGenes = geneList[[1]],
> annot = annFUN.gene2GO, gene2GO = gene2GO))
>
> and submit this topGOdata object to the following:
>
> test.stat.BP <- list()
> result.BP <- list()
> test.stat.BP[1] <- list(new("classicCount", testStatistic = GOFisherTest, name = "Fisher test"))
> result.BP[1] <- list(getSigGroups(BP.GOdata, test.stat.BP[[1]]))
> test.stat.BP[2] <- list(new("elimCount", testStatistic = GOFisherTest, name = "Fisher test", cutOff = 0.01))
> result.BP[2] <- list(getSigGroups(BP.GOdata, test.stat.BP[[2]]))
> test.stat.BP[3] <- list(new("weightCount", testStatistic = GOFisherTest, name = "Fisher test", sigRatio = "ratio"))
> result.BP[3] <- list(getSigGroups(BP.GOdata, test.stat.BP[[3]]))
> l <- list(classic = score(result.BP[[1]]), elim = score(result.BP[[2]]), weight = score(result.BP[[3]]))
> allRes.BP <- genTable(BP.GOdata, l, orderBy = "classic", ranksOf = "classic", top = length(score(result.BP[[1]])))
>
> My resulting data.frame, allRes.BP, shows that for category GO:0006836, there are only 11 annotated Entrez Gene IDs, not 32. The call to genTable() does correctly find that 4 of these are significant.
>
> This latest released version of topGO must be using the Mar 14 11:46:06 2007 build of GO, and I assume biomaRt is more current as I did the query just today. If category GO:0006836, neurotransmitter transport, has grown from 11 EGs to 32 EGs between now and last March for Human, then everything is as it should be. But this seems unlikely to me. So I wonder if there is a bug in the topGO calculations.
>
> Here is my session:
>
>
> sessionInfo()
> R version 2.5.1 (2007-06-27)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base"
>
> other attached packages:
> goTools hgu133plus2 Rgraphviz geneplotter lattice topGO SparseM annotate GO graph Biobase biomaRt RCurl XML
> "1.8.0" "1.16.0" "1.14.1" "1.14.0" "0.15-11" "1.2.1" "0.73" "1.14.1" "1.16.0" "1.14.2" "1.14.1" "1.10.1" "0.8-0" "1.9-0"
>
> Thanks very much,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D. University of Washington
> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
> Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> http://staff.washington.edu/~dbeyer
>
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