DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
2
0
Entering edit mode
7.2 years ago
sangita_b ▴ 80

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 • 4.0k views
ADD COMMENT
0
Entering edit mode
7.2 years ago
Martombo ★ 3.0k

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.

ADD COMMENT
0
Entering edit mode
7.2 years ago

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"
ADD COMMENT

Login before adding your answer.

Traffic: 2738 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6