Question: Gene symbol convert to Entrez ID
2
gravatar for landscape95
3.4 years ago by
landscape95170
landscape95170 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 • 17k views
ADD COMMENTlink modified 2.1 years ago by zx87549.7k • written 3.4 years ago by landscape95170

In what way did BioMart not help?

ADD REPLYlink written 3.4 years ago by Emily_Ensembl21k
11
gravatar for russhh
3.4 years ago by
russhh5.5k
UK, U. Glasgow
russhh5.5k 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 3.4 years ago by russhh5.5k

Hello, I am a beginner in R. Can you tell me how to retrieve the output from this 'select' method into a data frame? Thanks!

ADD REPLYlink written 8 months ago by drshamy870
1

It returns a data.frame. In R you have to be pretty explicit about which function you are using, and the code above might fail if you have {dplyr} (or another package that exports a select function / method) loaded. If the above doesn't work, you could try AnnotationDbi::select() to make it more explicit which package's select function you want to use (org.Hs.eg.db implicitly imports AnnotationDbi and the select function from AnnotationDbi is dispatched on orgDb objects like org.Hs.eg.db).

ADD REPLYlink written 8 months ago by russhh5.5k
1

But, to store the data, just use assignment: gene_data <- AnnotationDbi::select(blah, blah, blah)

ADD REPLYlink written 8 months ago by russhh5.5k
2
gravatar for cpad0112
3.4 years ago by
cpad011214k
India
cpad011214k 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 2.1 years ago by zx87549.7k • written 3.4 years ago by cpad011214k
1
gravatar for Emily_Ensembl
3.4 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k 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 3.4 years ago by Emily_Ensembl21k

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

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by landscape95170
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 3.4 years ago by Denise CS5.1k
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