Question

topGO - genesInTerm returns genes not in the annotation

1

Entering edit mode

samuel collombet ▴ 140

@samuel-collombet-6574

Last seen 6.9 years ago

France

Hi,

I am using the topGO package and I got very strange results:

I made a go2genes list myself, downloading go annotation mapping ensembl gene id with biomart :

> mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",host="feb2014.archive.ensembl.org", path="/biomart/martservice", dataset="mmusculus_gene_ensembl")

> ensemblGene_go <- getBM(attributes=c("ensembl_gene_id","go_id","external_gene_id"),filters="ensembl_gene_id", values=ensembl$ensembl_geneID,mart=mart)
> head(ensemblGene_go )

     ensembl_gene_id      go_id external_gene_id
1 ENSMUSG00000013653 GO:0008150    1810065E05Rik
2 ENSMUSG00000013653 GO:0005575    1810065E05Rik
3 ENSMUSG00000013653 GO:0003674    1810065E05Rik
4 ENSMUSG00000058287 GO:0008150          Gm12253
5 ENSMUSG00000058287 GO:0046849          Gm12253
6 ENSMUSG00000058287 GO:0005575          Gm12253

> go2ensemblGene <- split(ensemblGene_go$ensembl_gene_id,ensemblGene_go$go_id)
> go2ensemblGene[1:2]

$`GO:0000002`
[1] "ENSMUSG00000022889" "ENSMUSG00000033845" "ENSMUSG00000030879"
[4] "ENSMUSG00000090262" "ENSMUSG00000019699" "ENSMUSG00000030557"
[7] "ENSMUSG00000027424"

$`GO:0000003`
[1] "ENSMUSG00000029061"

I then make my topGO object:

> GOdata <- new("topGOdata", ontology="BP", annot=annFUN.GO2genes, GO2genes=go2ensemblGene, allGenes=GeneList,nodeSize=5,geneSel=topClusterGenes)

Then, if I call genesInTerm() for some GO term, the mapping between genes and go term does not fit at all!

> genesInTerm(GOdata,"GO:0051053")
$`GO:0051053`
[1] "ENSMUSG00000022878" "ENSMUSG00000032633" "ENSMUSG00000036086"
[4] "ENSMUSG00000036986" "ENSMUSG00000045658" "ENSMUSG00000046323"
[7] "ENSMUSG00000046697" "ENSMUSG00000054272" "ENSMUSG00000056758"

> go2ensemblGene["GO:0051053"]
$`GO:0051053`
[1] "ENSMUSG00000026241" "ENSMUSG00000053647"

another example:

> genesInTerm(GOdata,"GO:0051055")
$`GO:0051055`
[1] "ENSMUSG00000025856" "ENSMUSG00000032715" "ENSMUSG00000033161"
[4] "ENSMUSG00000036856" "ENSMUSG00000047638"

> go2ensemblGene["GO:0051055"]
$`GO:0051055`
[1] "ENSMUSG00000041333" "ENSMUSG00000078686" "ENSMUSG00000094793"
[4] "ENSMUSG00000078675" "ENSMUSG00000078673" "ENSMUSG00000078672"

I guess I do something wrong when I create the topGO object, but I followed the vignette and my annotation seems alright...
Any idea?

topGO • 1.9k views

ADD COMMENT • link 9.1 years ago samuel collombet ▴ 140

0

Entering edit mode

If needed my sessionInfo:

> sessionInfo()
R version 3.1.0 RC (2014-04-05 r65382)
Platform: x86_64-pc-linux-gnu (64-bit)

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=en_US.UTF-8    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] tcltk     grid      parallel  stats4    stats     graphics  grDevices
 [8] utils     datasets  methods   base     

other attached packages:
 [1] topGO_2.18.0              SparseM_1.6              
 [3] GO.db_3.0.0               RSQLite_1.0.0            
 [5] DBI_0.3.1                 AnnotationDbi_1.28.1     
 [7] graph_1.44.1              biomaRt_2.22.0           
 [9] Mfuzz_2.26.0              DynDoc_1.44.0            
[11] widgetTools_1.44.0        e1071_1.6-4              
[13] Biobase_2.26.0            wq_0.4-1                 
[15] zoo_1.7-12                reshape2_1.4.1           
[17] ggplot2_1.0.1             RColorBrewer_1.1-2       
[19] DESeq2_1.6.3              RcppArmadillo_0.4.650.1.1
[21] Rcpp_0.11.5               GenomicRanges_1.18.4     
[23] GenomeInfoDb_1.2.4        IRanges_2.0.1            
[25] S4Vectors_0.4.0           BiocGenerics_0.12.1      

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     annotate_1.44.0     base64enc_0.1-2    
 [4] BatchJobs_1.5       BBmisc_1.9          BiocParallel_1.0.3 
 [7] bitops_1.0-6        brew_1.0-6          checkmate_1.5.1    
[10] class_7.3-12        cluster_2.0.1       codetools_0.2-11   
[13] colorspace_1.2-6    digest_0.6.8        fail_1.2           
[16] foreach_1.4.2       foreign_0.8-63      Formula_1.2-0      
[19] genefilter_1.48.1   geneplotter_1.44.0  gtable_0.1.2       
[22] Hmisc_3.15-0        iterators_1.0.7     lattice_0.20-30    
[25] latticeExtra_0.6-26 locfit_1.5-9.1      MASS_7.3-39        
[28] munsell_0.4.2       nnet_7.3-9          plyr_1.8.1         
[31] proto_0.3-10        RCurl_1.95-4.5      rpart_4.1-9        
[34] scales_0.2.4        sendmailR_1.2-1     splines_3.1.0      
[37] stringr_0.6.2       survival_2.38-1     tkWidgets_1.44.0   
[40] tools_3.1.0         XML_3.98-1.1        xtable_1.7-4       
[43] XVector_0.6.0      
>

ADD REPLY • link 9.1 years ago samuel collombet ▴ 140