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Old 01-18-2011, 03:33 AM   #1
NicoBxl
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Default Ensembl id conversion

Hi,

I've a list of ensembl id ( from Bos Taurus )

How can I convert this ids to entrez id or gene symbol per example ?

Thanks

N.
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Old 01-18-2011, 04:49 AM   #2
gaffa
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You could try UniProt's ID Mapping service (http://www.uniprot.org/ -> "ID Mapping" tab).
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Old 01-19-2011, 03:19 AM   #3
whsqwghlm
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Or BioMart; http://www.ensembl.org/biomart/martview
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Old 01-19-2011, 04:05 AM   #4
dariober
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If you are willing to go for R/Bioconductor this might help:

Code:
library(biomaRt)
mart<- useDataset("btaurus_gene_ensembl", useMart("ensembl"))

ensembl_genes<- c("ENSBTAG00000026199", "ENSBTAG00000014685") ## etc...

getBM(
  filters= "ensembl_gene_id", 
  attributes= c("ensembl_gene_id", "external_gene_id", "entrezgene", "description"),
  values= ensembl_genes,
  mart= mart)

     ensembl_gene_id external_gene_id entrezgene                                                                                                           description
1 ENSBTAG00000014685       HPRT_BOVIN     613512 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
2 ENSBTAG00000014685       HPRT_BOVIN     510369 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
3 ENSBTAG00000014685       HPRT_BOVIN     281229 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
4 ENSBTAG00000014685       HPRT_BOVIN         NA Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
5 ENSBTAG00000026199     Q862P9_BOVIN     280979                                                Bos taurus actin, beta (ACTB), mRNA. [Source:RefSeq DNA;Acc:NM_173979]
>
Dario
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Old 01-19-2011, 04:06 AM   #5
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thanks it's perfect !
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Old 02-05-2013, 10:24 AM   #6
vkartha
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Quote:
Originally Posted by dariober View Post
If you are willing to go for R/Bioconductor this might help:

Code:
library(biomaRt)
mart<- useDataset("btaurus_gene_ensembl", useMart("ensembl"))

ensembl_genes<- c("ENSBTAG00000026199", "ENSBTAG00000014685") ## etc...

getBM(
  filters= "ensembl_gene_id", 
  attributes= c("ensembl_gene_id", "external_gene_id", "entrezgene", "description"),
  values= ensembl_genes,
  mart= mart)

     ensembl_gene_id external_gene_id entrezgene                                                                                                           description
1 ENSBTAG00000014685       HPRT_BOVIN     613512 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
2 ENSBTAG00000014685       HPRT_BOVIN     510369 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
3 ENSBTAG00000014685       HPRT_BOVIN     281229 Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
4 ENSBTAG00000014685       HPRT_BOVIN         NA Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase)(HGPRT)(EC 2.4.2.8) [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ18]
5 ENSBTAG00000026199     Q862P9_BOVIN     280979                                                Bos taurus actin, beta (ACTB), mRNA. [Source:RefSeq DNA;Acc:NM_173979]
>
Dario

I try the same thing, but I don't get any results:

library(biomaRt)
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))

genes<-c("ENSG00000000003.10","ENSG00000000005.5","ENSG00000000419.8","ENSG00000000457.8","ENSG00000000460.11"))

getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id", "entrezgene", "description"),values=genes,mart= mart)

[1] ensembl_gene_id entrezgene description
<0 rows> (or 0-length row.names)
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Old 02-05-2013, 11:36 PM   #7
dariober
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Quote:
Originally Posted by vkartha View Post
I try the same thing, but I don't get any results:

library(biomaRt)
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))

genes<-c("ENSG00000000003.10","ENSG00000000005.5","ENSG00000000419.8","ENSG00000000457.8","ENSG00000000460.11"))

getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id", "entrezgene", "description"),values=genes,mart= mart)

[1] ensembl_gene_id entrezgene description
<0 rows> (or 0-length row.names)
I suspect the ensembl gene id should not include the "decimal" part (ENSG00000000003 instead of ENSG00000000003.10).
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Old 08-08-2013, 07:37 AM   #8
zn_ab2010@yahoo.com
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Default convert GI to Entrez

hi, i have a list of genes from NCBI. does anyone know how to convert GI to Entrez?
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Old 08-08-2013, 08:06 AM   #9
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Quote:
Originally Posted by zn_ab2010@yahoo.com View Post
hi, i have a list of genes from NCBI. does anyone know how to convert GI to Entrez?
That's pretty easy to do in R with the various org.XX.eg.db packages (where XX is the abbreviation for whatever organism you're using).
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Old 05-08-2014, 05:07 AM   #10
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Quote:
Originally Posted by dpryan View Post
That's pretty easy to do in R with the various org.XX.eg.db packages (where XX is the abbreviation for whatever organism you're using).

If I use Biomart http://www.ensembl.org/biomart/martview/ , is it better than R package (org.XX.eg.db )?

Last edited by super0925; 05-08-2014 at 05:45 AM.
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Old 05-08-2014, 06:23 AM   #11
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It might be more updated, though there's no guarantee there.
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Old 05-08-2014, 08:04 AM   #12
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Quote:
Originally Posted by dpryan View Post
It might be more updated, though there's no guarantee there.
Hi if I have a list of genes by Ensembl ID or Gene namein cows, I want to covert them to human Ensembl ID and Gene name. I could do it by website http://www.ensembl.org/biomart/martview/ I know how to do it .
But it is not automatically. Could you please recommend a R package to achieve the Gene-ID converter?
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Old 05-08-2014, 09:41 AM   #13
dpryan
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There's a biomaRt package that's an interface to biomart, but aside from that I'm not aware of anything. Of course, this isn't something that I ever need to do, so me not knowing of a package for it doesn't mean much.
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Old 05-08-2014, 10:06 AM   #14
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Quote:
Originally Posted by dpryan View Post
There's a biomaRt package that's an interface to biomart, but aside from that I'm not aware of anything. Of course, this isn't something that I ever need to do, so me not knowing of a package for it doesn't mean much.
Thank you !I will try to download that package and try it.
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