how to find ensembl genes belonging to a GO category?
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Entering edit mode
Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 3 days ago
Wageningen University, Wageningen, the …

Hi,

I have a list of Gene Ontology IDs, and I would like to extract the genes (ensembl IDs) that belong to these GO terms. To do this I would like to use the biomaRt package. However, I cannot get it to work; i get an error indicating an invalid filter is used. This also happens when running an example from the vignette.... Apparently 'go_id' nor 'go' are good names for the GO filter anymore....? I would appreciate some assistance with this.

Thanks, Guido

 

library("biomaRt")
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

# example from vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html#retrieve-all-hugo-gene-symbols-of-genes-that-are-located-on-chromosomes-1720-or-y-and-are-associated-with-specific-go-terms

go=c("GO:0051330","GO:0000080","GO:0000114","GO:0000082")
chrom=c(17,20,"Y")
getBM(attributes= "hgnc_symbol",
        filters=c("go_id","chromosome_name"),
        values=list(go, chrom), mart=ensembl)

Error in getBM(attributes = "hgnc_symbol", filters = c("go_id", "chromosome_name"),  :
  Invalid filters(s): go_id
Please use the function 'listFilters' to get valid filter names

# listFilters finds this gene ontology idetifier, but doesn't work either...:

> listFilters(ensembl)[82,]
   name                description
82   go GO ID(s) [e.g. GO:0000002]

 

 

> sessionInfo()
R version 3.5.1 Patched (2018-08-13 r75130)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.36.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18         AnnotationDbi_1.42.1 magrittr_1.5         BiocGenerics_0.26.0
 [5] hms_0.4.2            progress_1.2.0       IRanges_2.14.12      bit_1.1-14          
 [9] R6_2.2.2             rlang_0.2.2          httr_1.3.1           stringr_1.3.1       
[13] blob_1.1.1           tools_3.5.1          parallel_3.5.1       Biobase_2.40.0      
[17] DBI_1.0.0            bit64_0.9-7          digest_0.6.17        assertthat_0.2.0    
[21] crayon_1.3.4         S4Vectors_0.18.3     bitops_1.0-6         RCurl_1.95-4.11     
[25] memoise_1.1.0        RSQLite_2.1.1        stringi_1.2.4        compiler_3.5.1      
[29] prettyunits_1.0.2    stats4_3.5.1         XML_3.98-1.16        pkgconfig_2.0.2     
>

 

biomart gene ontology GO • 3.7k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
> getBM(c("go_id","ensembl_gene_id"), "go", go, mart)
          go_id ensembl_gene_id
1    GO:0003723 ENSG00000206557
2    GO:0005737 ENSG00000206557
3    GO:0008270 ENSG00000206557
4    GO:0046872 ENSG00000206557
5    GO:0016740 ENSG00000206557

<snip>

But then what you say you want to do (get Ensembl Gene IDs for GO terms) and what your code is trying to do (get HUGO gene symbols based on a weird combination of GO ID and chromosome?) are not the same thing. Howeva,

> getBM(c("go_id","ensembl_gene_id","hgnc_symbol"), c("go", "chromosome_name"), list(go, chrom), mart)
         go_id ensembl_gene_id hgnc_symbol
1   GO:0005634 ENSG00000108443     RPS6KB1
2   GO:0005737 ENSG00000108443     RPS6KB1
3   GO:0016020 ENSG00000108443     RPS6KB1
4   GO:0000166 ENSG00000108443     RPS6KB1
5   GO:0004672 ENSG00000108443     RPS6KB1
6   GO:0004674 ENSG00000108443     RPS6KB1
7   GO:0005524 ENSG00000108443     RPS6KB1
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Entering edit mode

In fairness to the OP the example does state it comes from the biomaRt vignette & fails in the same manner.   I've updated the devel vignette with the correct filter name now.

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Entering edit mode

Thanks for the pointers; got it working.

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