Get Gene Onthology information for NCBI GeneIDs - Apis mellifera (honey bee)

Question

[mschmid]

I am performing a RNAseq-analysis. I have my DE expressed genes. Now I want to perform a GO term enrichment analysis.

I have the NCBI GeneIDs for the DE genes as well as for the "background" genes. I want to use Bioconductor tool "goseq". So I have to get the corresponding GO terms for my genes. My genome is Apis mellifera (honey bee): https://www.ncbi.nlm.nih.gov/assembly/GCA_003254395.2

How can I get the corresponding GO terms for my genes? Should be possible but I do not find a way.

Answer 1

[Kevin Blighe]

Hey,

You can do this with biomaRt in R:

require(biomaRt)

mart <- useMart('metazoa_mart', host = 'metazoa.ensembl.org') 
mart <- useDataset('amellifera_eg_gene', mart)

annot <- getBM(
  mart = mart,
  attributes = c(
    'entrezgene_id',
    'ensembl_gene_id',
    'external_gene_name',
    'gene_biotype',
    'go_id',
    'name_1006'),
  uniqueRows = TRUE)

annot then contains the following:

head(annot, 20)

entrezgene_id   ensembl_gene_id   external_gene_name   gene_biotype    go_id        name_1006
NA              GB41543                                protein_coding  GO:0046872   metal ion binding
NA              GB41543                                protein_coding  GO:0020037   heme binding
NA              GB41543                                protein_coding  GO:0005344   oxygen carrier activity
NA              GB41543                                protein_coding  GO:0015671   oxygen transport
NA              GB54642                                protein_coding  GO:0005525   GTP binding

The Entrez (NCBI) gene IDs and external gene names are there for some:

head(annot$entrezgene_id[!is.na(annot$entrezgene_id)], 10)
 [1] 100576508 100576508 107965534    726750    725548 100576425 100576425    410109    410109    410109

head(annot$external_gene_name[annot$external_gene_name!=''], 10)
 [1] "AME.4465" "OBP9"     "GE-1"     "CED-6"    "EF1BETA"  "EF1BETA"  "MRPS14"   "MRPS14"   "MRPS14"   "MRPS14"

Run listAttributes(mart) in order to see what else you can bring into the annotation table.

Kevin