Question: Gene symbol convert to Entrez ID
2
gravatar for landscape95
2.3 years ago by
landscape95160
landscape95160 wrote:

Can somebody help me in converting Gene name to Entrez in R. For example

Gene name: ANKRD62P1-PARP4P3 has entrez: 23783

like this page:

http://www.genecards.org/cgi-bin/carddisp.pl?gene=ANKRD62P1-PARP4P3&keywords=ANKRD62P1-PARP4P3

I tried biomaRt but it didn't have the gene (return to NA)!

I tried this:

ensembl=useDataset("hsapiens_gene_ensembl",mart = useMart("ensembl"))

  data = "ANKRD62P1-PARP4P3"
  ans <- unique(getBM(attributes = c("hgnc_symbol", "entrezgene"),    
                      filters = "hgnc_symbol",
                      values = data,
                      mart = ensembl) )

Your help is really appreciated!

entrez biomart R • 9.7k views
ADD COMMENTlink modified 12 months ago by zx87548.2k • written 2.3 years ago by landscape95160

In what way did BioMart not help?

ADD REPLYlink written 2.3 years ago by Emily_Ensembl19k
9
gravatar for russhh
2.3 years ago by
russhh4.7k
UK, U. Glasgow
russhh4.7k wrote:

I'd just use org.Hs.eg.db if it's a mapping within EntrezGene that you're interested in.

library(org.Hs.eg.db)
hs <- org.Hs.eg.db
my.symbols <- c("ANKRD62P1-PARP4P3")
select(hs, 
       keys = my.symbols,
       columns = c("ENTREZID", "SYMBOL"),
       keytype = "SYMBOL")
#              SYMBOL ENTREZID
# 1 ANKRD62P1-PARP4P3    23783
ADD COMMENTlink written 2.3 years ago by russhh4.7k
1
gravatar for Emily_Ensembl
2.3 years ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

It didn't work in BioMart because Ensembl does not have the link between ANKRD62P1-PARP4P3 and 23783, since they have different biotypes: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000189295;r=22:16654066-16675540

ADD COMMENTlink written 2.3 years ago by Emily_Ensembl19k

Thank you! Is there any other way to get its entrez number?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by landscape95160
1

How many genes (or pseudogene) you can't get the corresponding ID with biomaRt? I've looked at the pseudogene json files from HGNC and can not find a gene named ANKRD62P1-PARP4P3, although they do list ANKRD62P1-PARP4P3 as a pseudogene, which corresponds to Entrez 23783. There is a HGNC BioMart but no Entrez IDs as an attribute (or filter for that matter).

ADD REPLYlink written 2.3 years ago by Denise - Open Targets5.0k
1
gravatar for cpad0112
2.3 years ago by
cpad011211k
India
cpad011211k wrote:
library(EnsDb.Hsapiens.v86)

hsens=EnsDb.Hsapiens.v86
my.symbols <- c("ANKRD62P1-PARP4P3")

select(hsens,  
       keys = my.symbols, 
       columns = c("ENTREZID", "SYMBOL", "GENEID"), 
       keytype = "SYMBOL")


# ENTREZID              SYMBOL          GENEID
# 1          ANKRD62P1-PARP4P3 ENSG00000189295
ADD COMMENTlink modified 12 months ago by zx87548.2k • written 2.3 years ago by cpad011211k
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