Hi, Please I have searched alot but none of the solutions I have seen has fully been helpful. I want to convert a list of >20k genes names to Ensemble ID. Any script/tool/guide would really be helpful.
Thanks
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written
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bazok •
As the organism is not mentioned I'm sharing a R snippet with human as a placeholder.
library("AnnotationDbi")
library("org.Hs.eg.db")
df$ensid = mapIds(org.Hs.eg.db,
keys=df$symbol,
column="ENSEMBL",
keytype="SYMBOL",
multiVals="first")
Thanks Arup! It's good to have both the biomaRt and AnnotationDbi solutions. Judging by the question title, this particular question will be picked up extensively by search engines
Thanks alot, with the above and hints from the below link, I was able to convert around 20k gene symbols to ensembl. there are 3.3k that returned "NA". I tried biomaRt to recover the remaining 3.3k but I keep getting error (Error in bmRequest(request = request, verbose = verbose) : Internal Server Error (HTTP 500) which I am still not able to resolve. Any help will be appreciated.
Can't fetch pathways by entrez id?
Regards
Assuming that you have HGNC symbols, you can achieve this via biomaRt in R:
require('biomaRt')
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
mart = mart,
attributes = c(
'hgnc_symbol',
'ensembl_gene_id',
'gene_biotype'),
uniqueRows = TRUE)
head(annotLookup)
hgnc_symbol ensembl_gene_id gene_biotype
1 MT-TF ENSG00000210049 Mt_tRNA
2 MT-RNR1 ENSG00000211459 Mt_rRNA
3 MT-TV ENSG00000210077 Mt_tRNA
4 MT-RNR2 ENSG00000210082 Mt_rRNA
5 MT-TL1 ENSG00000209082 Mt_tRNA
6 MT-ND1 ENSG00000198888 protein_coding
tail(annotLookup)
hgnc_symbol ensembl_gene_id gene_biotype
67142 ENSG00000285949 lncRNA
67143 ENSG00000284921 lncRNA
67144 ENSG00000285440 processed_pseudogene
67145 ENSG00000285110 processed_pseudogene
67146 MTRF1LP2 ENSG00000285363 processed_pseudogene
67147 GSDMC ENSG00000285114 protein_coding
tail(subset(annotLookup, hgnc_symbol != ''))
hgnc_symbol ensembl_gene_id gene_biotype
67137 RNU6-1233P ENSG00000285461 snRNA
67139 RUVBL1 ENSG00000284901 protein_coding
67140 RNU6-823P ENSG00000284805 snRNA
67141 EEFSEC ENSG00000284869 protein_coding
67146 MTRF1LP2 ENSG00000285363 processed_pseudogene
67147 GSDMC ENSG00000285114 protein_coding
Then, use annotLookup as a lookup table for your genes.
Kevin
Hi, you just need to read the data into R via read.csv() or read.table(). There, you can match your genes to the output contained in annotLookup.
However, it seems that your problem has now been resolved.
Hi, sometimes there is a problem with the Ensembl 'mirror' that is automatically chosen by biomaRt. Please try the same code but with this line:
mart <- useMart('ENSEMBL_MART_ENSEMBL', host = 'uswest.ensembl.org')
This is perfect Kevin, thanks!
Using Enembl REST API:
http://rest.ensembl.org/lookup/symbol/homo_sapiens/A1CF
assembly_name: GRCh38
biotype: protein_coding
db_type: core
description: APOBEC1 complementation factor [Source:HGNC Symbol;Acc:HGNC:24086]
display_name: A1CF
end: 50885675
id: ENSG00000148584
logic_name: ensembl_havana_gene_homo_sapiens
object_type: Gene
seq_region_name: 10
source: ensembl_havana
species: homo_sapiens
start: 50799409
strand: -1
version: 15
http://rest.ensembl.org/lookup/symbol/homo_sapiens/A1CF?content-type=application/json
{"strand":-1,"assembly_name":"GRCh38","version":15,"species":"homo_sapiens","end":50885675,"description":"APOBEC1 complementation factor [Source:HGNC Symbol;Acc:HGNC:24086]","source":"ensembl_havana","db_type":"core","object_type":"Gene","id":"ENSG00000148584","seq_region_name":"10","display_name":"A1CF","start":50799409,"logic_name":"ensembl_havana_gene_homo_sapiens","biotype":"protein_coding"}
Look up multiple symbols at one time:
$ wget -q --header='Content-type:application/json' --header='Accept:application/json' --post-data='{ "symbols" : ["A1BG","A1BG-AS1","A1CF" ] }' 'http://rest.ensembl.org/lookup/symbol/homo_sapiens' -O -
{"A1CF":{"object_type":"Gene","version":15,"db_type":"core","seq_region_name":"10","end":50885675,"display_name":"A1CF","id":"ENSG00000148584","assembly_name":"GRCh38","source":"ensembl_havana","biotype":"protein_coding","start":50799409,"strand":-1,"logic_name":"ensembl_havana_gene_homo_sapiens","species":"homo_sapiens","description":"APOBEC1 complementation factor [Source:HGNC Symbol;Acc:HGNC:24086]"},"A1BG-AS1":{"start":58347718,"strand":1,"logic_name":"havana_homo_sapiens","species":"homo_sapiens","description":"A1BG antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:37133]","source":"havana","biotype":"lncRNA","id":"ENSG00000268895","assembly_name":"GRCh38","object_type":"Gene","version":6,"seq_region_name":"19","db_type":"core","end":58355455,"display_name":"A1BG-AS1"},"A1BG":{"description":"alpha-1-B glycoprotein [Source:HGNC Symbol;Acc:HGNC:5]","logic_name":"ensembl_havana_gene_homo_sapiens","species":"homo_sapiens","strand":-1,"start":58345178,"biotype":"protein_coding","source":"ensembl_havana","assembly_name":"GRCh38","id":"ENSG00000121410","display_name":"A1BG","seq_region_name":"19","version":12,"end":58353492,"db_type":"core","object_type":"Gene"}}
Hello, here is some way I know.
1. R package org.Hs.eg.db, this package contains mapping between gene IDs, like SYMBOL, entrez ID, Ensembl ID.
2. R package biomaRt, this package helps you query information(including gene ID mapping) from BioMart.
3. You can download gene ID data from BioMart. Select Ensembl Genes 99 --> Human genes --> Attributes --> GENE --> External References --> select HGNC symbol and NCBI gene ID --> Results. If you don't know how to use R, you can use this file with other language.
[Yet] Another method here, by Pierre: A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Hey! A bit late to the party! I’ve built a simple wrapper (named SESC) around biomaRt to streamline Ensembl ID conversions. It supports both single queries for quick lookups and batch conversions for larger datasets.
Single Mode
Rscript SESC_v0.1.R -m single -q ENSG00000012048 -a ensembl_gene_id,hgnc_symbol -f ensembl_gene_id -o stdout
Batch Mode
Rscript SESC_v0.1.R -m batch -i test_batch.txt -a ensembl_gene_id,hgnc_symbol -f ensembl_gene_id -o test_batch_output.txt
GitHub Repo: https://github.com/Thanujay/SESC
Thank you!
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Hello. Please paste a sample of the gene names that you have, and state the species, which will also help.
Hi, Few of the gene names/symbol are below. A1BG,A1BG-AS1,A1CF,A2M,A2M-AS1,A2ML1,A2MP1,A3GALT2,A4GALT,A4GNT
Thanks
Thanks. These seem to be HGNC symbols. Both solutions below should help you. Please take time to check.
Thanks all for the inputs, I will run through them and feedback.
Regards