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
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 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
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
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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