Conversion of Gene Name to Ensembl ID

Question

[bazok]

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

[Kevin Blighe]

Hello. Please paste a sample of the gene names that you have, and state the species, which will also help.

[bazok]

Hi, Few of the gene names/symbol are below. A1BG,A1BG-AS1,A1CF,A2M,A2M-AS1,A2ML1,A2MP1,A3GALT2,A4GALT,A4GNT

Thanks

[Kevin Blighe]

Thanks. These seem to be HGNC symbols. Both solutions below should help you. Please take time to check.

[bazok]

Thanks all for the inputs, I will run through them and feedback.

Regards

Answer 1

[Arup Ghosh]

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")

[Kevin Blighe]

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

[bazok]

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

Answer 2

[Kevin Blighe]

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

[Nat.Nataren]

This is perfect Kevin, thanks!

[bazok]

Hi Kevin, Could you please elaborate a little on how to use the annotLookup. Suppose i have an input file- "genelist.csv"?

Thanks

[Kevin Blighe]

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.

[bazok]

Hi Kevin, Thanks for the reply. Yes, i was able to get past that but I still run into an error (Error in bmRequest(request = request, verbose = verbose) : Internal Server Error (HTTP 500) . I am still not able to fix this to convert the remaining 3.3k gene codes.

[Kevin Blighe]

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')

Answer 3

[GenoMax]

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"}}

Answer 4

[MatthewP]

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.

Answer 5

[Kevin Blighe]

[Yet] Another method here, by Pierre: A: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates

Answer 6

[Thanujay S]

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!