This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.

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

rna-seq deseq2 gene id ensembl id software
• 6,052 views • link
updated by Martombo Martombo • written by sangita_b sangita_b

2 answers

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.

• 0 views • link
updated by Ram Ram • written by Martombo Martombo

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"
• 0 views • link
updated by Ram Ram • written by cpad0112 cpad0112

Log in to answer this question.

More posts like this