Cannot annotate bacterial gene IDs via R (None of the keys entered are valid keys for 'ENSEMBL')

Question

[Mir-Mammad]

I have generated an excel spreadsheet using DESEQ2 and trying to convert bacterial (Streptococcus gordonii) geneIDs to gene names.

> readfile$symbol<-mapIds(org.Hs.eg.db, keys = row.names(readfile), keytype = "ENSEMBL", column = "SYMBOL") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

This is what my geneIDs look like:

SGO_0387
SGO_0749
SGO_0955
SGO_2105
SGO_0524
SGO_2076
SGO_0522
SGO_0217
SGO_0267
SGO_0711
SGO_0561

I assume that I am using the wrong database, but I do not understand where those IDs belong to as they appear on ENSEMBL, NCBI and Uniprot.

[iraun]

org.Hs.eg.db database is for human (see org.Hs.eg.db), no wonder why the bacterial IDs are not mapping :). You would have to find the equivalent for your species, or maybe use other method for the ID conversion.

[Mir-Mammad]

Thank you!

Answer 1

[GenoMax]

Those ID's only appear to be present in a specific genome (there are multiple genomes available for this organism) that is here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/017/005/GCF_000017005.1_ASM1700v1/

Unfortunately there are no gene names associated with these locus tags:

$ zgrep SGO_0387 GCF_000017005.1_ASM1700v1_genomic.gtf.gz 

NC_009785.1     RefSeq  gene    422921  423955  .       +       .       gene_id "SGO_RS01930"; transcript_id ""; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "SGO_RS01930"; old_locus_tag "SGO_0387"; 

You may want/need to consider using a different genome unless you want to annotate the gene names yourself. Not a trivial task.

[Mir-Mammad]

Thanks! What about GO enrichment analysis? I am basically reducing the experiment with the data from one of the papers, and they were able to perform go enrichment analysis on the same genome.