Gene symbol convert to Entrez ID

Question

[landscape95]

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!

[Emily]

In what way did BioMart not help?

Answer 1

[russhh]

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

[drshamy87]

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!

[russhh]

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).

[russhh]

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

[vipulwagh31]

@russhh 'org.Hs.eg.db' works well with few genes. I have approx 17k genes, and I wish to convert these gene symbols to entrez ids. I tried submitting the entire list and I get the following error:

library(org.Hs.eg.db) library(AnnotationDbi)

hs <- org.Hs.eg.db my.symbols=myData$Symbols AnnotationDbi::select (hs, + keys = my.symbols, + columns = c("ENTREZID", "SYMBOL"), + keytype = "SYMBOL") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.

The input file looks like this:

head(my.symbols) [1] " TTLL10 " " B3GALT6 " " SCNN1D " " PUSL1 " " VWA1 " " ATAD3C " class(my.symbols) [1] "character" class(myData) [1] "data.frame"

I tried submitting one of the genes as mentioned above in one of your response and it works well:

hs <- org.Hs.eg.db one.symbol=c("TTLL10") AnnotationDbi::select (hs, + keys = one.symbol, + columns = c("ENTREZID", "SYMBOL"), + keytype = "SYMBOL") 'select()' returned 1:1 mapping between keys and columns SYMBOL ENTREZID 1 TTLL10 254173

Any suggestions on how can I get entrezids for multiple genes at once?

I also tried using biomart, and I am facing an issue with it too. Do you think there is a mistake in the way I am submitting the gene list? Here is the code for biomart:

For one gene (biomart)

library(biomaRt) mart <- useMart("ENSEMBL_MART_ENSEMBL") mart <- useDataset("hsapiens_gene_ensembl", mart) one.symbol_b= c("TTLL10")

annotLookup <- getBM( + mart=mart, + attributes=c("entrezgene_id", "hgnc_symbol"), filter = "hgnc_symbol", + values = one.symbol_b) head(annotLookup) entrezgene_id hgnc_symbol 1 254173 TTLL10

For the entire gene list from a dataframe (>17k gene symbols) (biomart)

mart <- useMart("ENSEMBL_MART_ENSEMBL") mart <- useDataset("hsapiens_gene_ensembl", mart)

my.symbols_b= my.Data$Symbols

annotLookup <- getBM( + mart=mart, + attributes=c("entrezgene_id", "hgnc_symbol"), filter = "hgnc_symbol", + values = my.symbols_b)

head(annotLookup) [1] entrezgene_id hgnc_symbol
<0 rows> (or 0-length row.names)

I have no clue where I am going wrong. It will be really helpful if you could guide me in the right direction.

Thanks in advance.

Answer 2

[Emily]

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

[landscape95]

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

[Denise CS]

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).

Answer 3

[cpad0112]

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