Question: DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
0
gravatar for sangita_b
2.8 years ago by
sangita_b70
United Kingdom
sangita_b70 wrote:

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

ADD COMMENTlink modified 2.8 years ago by Martombo2.1k • written 2.8 years ago by sangita_b70
0
gravatar for Martombo
2.8 years ago by
Martombo2.1k
Seville, ES
Martombo2.1k wrote:

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 COMMENTlink modified 2.8 years ago • written 2.8 years ago by Martombo2.1k
0
gravatar for cpad0112
2.8 years ago by
cpad01127.7k
India
cpad01127.7k wrote:

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 COMMENTlink modified 2.8 years ago • written 2.8 years ago by cpad01127.7k
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