Get a bunch of ENTREZID into gene symbols

Question

[Kai_Qi]

Hi: Can anyone tell me some ways to convert ENTREZID into gene symbols. I get 450 or so ENTREZIDs after RNA-seq analysis in ER fraction. I want to convert them into gene symbols. I have tried DAVID gene conversion tools, but I only get 375 output even I input 450 there. Don't know why.

Thanks,

Cai

Answer 1

[piyushjo]

Try biomart.

Website

https://useast.ensembl.org/info/data/biomart/index.html

R package

https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

Use Gene symbol as filter and then entrez id as attribute.

[Kai_Qi]

The biomart approach worked it out. Thank you!

[Ram]

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Answer 2

[Ram]

Use org.Hs.eg.db in R. You should be able to use mapIds to get what you need. It is perfectly normal for the output to have more or fewer rows than the input, based on mapping between the IDs involved, but EntrezIDs -> HGNC symbols should be 1 to 0 or 1 mapping, so you should not see more output rows than input rows.