Question: Ensembl ID to ENTREZ best converter
0
gravatar for Morris_Chair
9 months ago by
Morris_Chair230
Morris_Chair230 wrote:

Hello everyone,

I used different tools to convert human gene ensemble ID to ENTREZ but each of them seems to have problems like: -BioMart does not recognizes all the ensemble ID but barely 30% , -BioDBnet ...I couldn't make it working cause I could only select the type of output , -DAVID gives me lots of false duplicates.

What do you usually use for this work ?

thank you

gene • 1.7k views
ADD COMMENTlink modified 8 months ago by Arup Ghosh2.8k • written 9 months ago by Morris_Chair230
1

I use biomaRt (for ensembl to uniprot id conversion) and this works fine for me (not 100%, I still loose some ids, but this number is small). Maybe you could try to play around a bit with the "attributes" and "filters"?

ADD REPLYlink written 9 months ago by manaswwm130
1

BioMart does not recognizes all the ensemble ID but barely 30%

Please show code and data examples. This is highly unlikely if used properly since biomart directly connects to Ensembl.

ADD REPLYlink written 9 months ago by ATpoint46k

Hi ATpoint , here is the code

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "hsapiens_gene_ensembl",
                         host = "http://www.ensembl.org")

genes <- getBM(filters = "ensembl_gene_id",
               attributes = c("ensembl_gene_id","entrezgene_id"),
               values = new_rowname, 
               mart = mart)

Probably there is something wrong with my hosting service?

Thank you

ADD REPLYlink written 9 months ago by Morris_Chair230
3

Provide examples of identifiers that don't seem to map. It would also help to know where these ID's came from.

ADD REPLYlink modified 9 months ago • written 9 months ago by GenoMax96k

Thank you genomax, indeed.. most of them are non-coding RNA :)

ADD REPLYlink written 8 months ago by Morris_Chair230
1

BioMart, as others have mentioned, tends to work pretty well. Have you removed the version numbers off the end of the ensembl ID? (ie 1234567.89 --> 1234567)

ADD REPLYlink written 9 months ago by aaragak140

Hi aaragak1, yes I did,

thanks

ADD REPLYlink written 9 months ago by Morris_Chair230

yes I did that, thanks :)

ADD REPLYlink written 8 months ago by Morris_Chair230
1

Are the ensembl IDs that you are working with derived from the current ensembl release?

ADD REPLYlink written 8 months ago by russhh5.5k

Hi russh, yes they are thx, problem solved anyways. Most of those ensemble where from non coding RNA

ADD REPLYlink written 8 months ago by Morris_Chair230
3
gravatar for Arup Ghosh
8 months ago by
Arup Ghosh2.8k
India
Arup Ghosh2.8k wrote:

You can use AnnotationDbi to convert Ensembl ids. The code snippet converts Ensembl id to Entrez ids.

library("AnnotationDbi")
library("org.Hs.eg.db")
#columns(org.Hs.eg.db) # returns list of available keytypes
data$entrez = mapIds(org.Hs.eg.db,
                    keys=row.names(data), 
                    column="ENTREZID",
                    keytype="ENSEMBL",
                    multiVals="first")
ADD COMMENTlink written 8 months ago by Arup Ghosh2.8k
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