DESEQ2: How can I convert ensembl gene id's to HGNC gene names.

Question

[sangita_b]

Hi

I have used DESeq2 to carry out differential gene expression analysis. My DESeq output contains ensembl gene id's. Is there a tool/ software package that I can use to convert these id's to gene names?

I have tried Biomart however it cannot convert the id's for the whole file (>60,000)

Thanks

Sangita

Answer 1

[Martombo]

Biomart should provide the correct solution to your problem and it should be able to convert all of the IDs, since it is provided by Ensembl itself. You should check what version of the Ensembl database was used for the gene expression analysis and use the same one for the IDs conversion. That's the only problem I can think of.

ps: this problem is not related to DESeq2, since the IDs are of course not elaborated by this program.

Answer 2

[cpad0112]

Did you try org.Hs.eg.db?

> columns(org.Hs.eg.db)
[1] "ENTREZID"     "PFAM"         "IPI"          "PROSITE"      "ACCNUM"     
[6] "ALIAS"        "CHR"          "CHRLOC"       "CHRLOCEND"    "ENZYME"     
[11] "MAP"          "PATH"         "PMID"         "REFSEQ"       "SYMBOL"     
[16] "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "GENENAME"   
[21] "UNIPROT"      "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"      
[26] "EVIDENCEALL"  "ONTOLOGYALL"  "OMIM"         "UCSCKG"     
> keytypes(org.Hs.eg.db)
[1] "ENTREZID"     "PFAM"         "IPI"          "PROSITE"      "ACCNUM"     
[6] "ALIAS"        "ENZYME"       "MAP"          "PATH"         "PMID"       
[11] "REFSEQ"       "SYMBOL"       "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"
[16] "ENSEMBLTRANS" "GENENAME"     "UNIPROT"      "GO"           "EVIDENCE"   
[21] "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL"  "OMIM"       
[26] "UCSCKG"