Question: mapping between gene symbol and entrez ID
0
gravatar for mike
23 months ago by
mike50
mike50 wrote:

Hello,

I have mapped a few gene symbols to their entrez IDs using:

library(org.Hs.eg.db) 

info4gene = select(org.Hs.eg.db, symbols, c("ENTREZID"), "ALIAS")

where symbols are the gene names, such as 'NUDT10'.

As below, why are they some gene symbols can map to more than two entrez IDs?

ALIAS   ENTREZID

NUDT10  53343

NUDT10  170685

Is this usual to have many to many mapping? Is there a way to give only one to one mapping?

Thank you!

ADD COMMENTlink modified 23 months ago • written 23 months ago by mike50

https://www.ncbi.nlm.nih.gov/gene/?term=NUDT10 In this case 'NUDT10' one gene symbol can have many alias, even on different chromosomes (chrX, chr4). How should the decision be made?

ADD REPLYlink written 23 months ago by mike50

53343 is NUDT9
170685 is NUDT10

ADD REPLYlink written 23 months ago by genomax76k

Yes, but NUDT10 is also the alias of 'NUDT9'. Also the command showed the same:

select(org.Hs.eg.db, "NUDT10", c("ENTREZID"), "ALIAS")
ADD REPLYlink written 23 months ago by mike50
2

Can you not use the primary gene name (instead of the alias)?

ADD REPLYlink written 23 months ago by genomax76k
1

Yes I think you should be using "SYMBOL" instead of "ALIAS"

ADD REPLYlink written 23 months ago by christopher medway440

Thank you, that worked!

ADD REPLYlink written 23 months ago by mike50
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