Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R

Question

[sugus]

I have a list of ensemble ID and I would like to convert them to gene symbol name. How am I supposed to do this in R?

[1] "ENSMUST00000110582" "ENSMUST00000110585" "ENSMUST00000110586" "ENSMUST00000135559"
 [5] "ENSMUST00000166082" "ENSMUST00000135552" "ENSMUST00000207020" "ENSMUST00000192677"
 [9] "ENSMUST00000090457" "ENSMUST00000207029"

I have tried using GPL20775-85955 annotation but only a few could be matched

Ginfo <- fread(file.path(data.path,"GPL20775-85955.txt"),sep = "\t",header = T,check.names = F,stringsAsFactors = F,data.table = F) 
Ginfo$ENSEMBLE <- sapply(strsplit(Ginfo$mrna_assignment, " // ", fixed = T), "[", 1)
Ginfo <- Ginfo[!duplicated(Ginfo$ENSEMBLE),]
rownames(Ginfo) <- Ginfo$ENSEMBLE
Ginfo$mrna <- sapply(strsplit(Ginfo$gene_assignment, " // ", fixed = T), "[", 2)

I think there may be a easier way to use bioMart or something but I do not know how.

Answer 1

[sugus]

I solved this.

mart <- useMart("ensembl","mmusculus_gene_ensembl")##人类选择hsapiens_gene_ensembl
ensemble2gene <- getBM(attributes=c("ensembl_transcript_id","external_gene_name","ensembl_gene_id"),
                       filters = "ensembl_transcript_id",
                       values = rownames(countsTable), 
                       mart = mart)
rownames(ensemble2gene) <- ensemble2gene$ensembl_transcript_id

[Kevin Blighe]

Awww, you beat me

Answer 2

[Kevin Blighe]

Hey friend, all good?

You can try org.Mm.eg.db and biomaRt. Let's see which one can map these:

lookup <- c('ENSMUST00000110582','ENSMUST00000110585',
  'ENSMUST00000110586','ENSMUST00000135559',
  'ENSMUST00000166082','ENSMUST00000135552',
  'ENSMUST00000207020','ENSMUST00000192677',
  'ENSMUST00000090457','ENSMUST00000207029')

org.Mm.eg.db

require('org.Mm.eg.db')
keytypes(org.Mm.eg.db)
select(
  org.Mm.eg.db,
  keytype = 'ENSEMBLTRANS',
  columns = c('ENSEMBL','ENSEMBLTRANS','ENTREZID','SYMBOL'),
  keys = lookup)

         ENSEMBLTRANS            ENSEMBL ENTREZID        SYMBOL
1  ENSMUST00000110582 ENSMUSG00000079083    77532          Jrkl
2  ENSMUST00000110585               <NA>     <NA>          <NA>
3  ENSMUST00000110586               <NA>     <NA>          <NA>
4  ENSMUST00000135559               <NA>     <NA>          <NA>
5  ENSMUST00000166082               <NA>     <NA>          <NA>
6  ENSMUST00000135552               <NA>     <NA>          <NA>
7  ENSMUST00000207020               <NA>     <NA>          <NA>
8  ENSMUST00000192677               <NA>     <NA>          <NA>
9  ENSMUST00000090457 ENSMUSG00000022543    74684 4930451G09Rik
10 ENSMUST00000207029               <NA>     <NA>          <NA>

biomaRt

library(biomaRt)
mart <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')

getBM(
  attributes = c(
    'ensembl_gene_id',
    'ensembl_transcript_id', 
    'entrezgene_id', 'mgi_symbol'),
  filters = 'ensembl_transcript_id',
  values = lookup,
  mart = mart)

      ensembl_gene_id ensembl_transcript_id entrezgene_id    mgi_symbol
1  ENSMUSG00000022543    ENSMUST00000090457         74684 4930451G09Rik
2  ENSMUSG00000079083    ENSMUST00000110582         77532          Jrkl
3  ENSMUSG00000054115    ENSMUST00000110585         27401          Skp2
4  ENSMUSG00000060227    ENSMUST00000110586        319996         Golm2
5  ENSMUSG00000020744    ENSMUST00000135552         67283      Slc25a19
6  ENSMUSG00000038271    ENSMUST00000135559        320678         Iffo1
7  ENSMUSG00000025512    ENSMUST00000166082         68038         Chid1
8  ENSMUSG00000034755    ENSMUST00000192677        245578       Pcdh11x
9  ENSMUSG00000058966    ENSMUST00000207020         68952        Tlcd3b
10 ENSMUSG00000109498    ENSMUST00000207029            NA       Gm45222

Kevin

[Nithya]

Dear Kevin, while running the following comments in R studio

lookup <- c('ENSMUST00000110582','ENSMUST00000110585','ENSMUST00000110586',

• 'ENSMUST00000135559','ENSMUST00000166082','ENSMUST00000135552',
• 'ENSMUST00000207020','ENSMUST00000192677','ENSMUST00000090457','ENSMUST00000207029') library(biomaRt) mart <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')

I am facing the this issue

Ensembl site unresponsive, trying uswest mirror Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: unable to get local issuer certificate

So, How I am supposed to come over this problem.

[Kevin Blighe]

Hi, this problem is related [I think] to 'overload' on Ensembl's side, and/or it could be that one or more greedy users are abusing their connection with Ensembl. You will just have to keep re-trying. Not much that I can do - sorry.

[Nithya]

That's fine.Thank you very much Mr. Kevin

[Nithya]

yes, Mr. Kevin, you are right There was a network issue. Today I got results.

 ensembl_gene_id ensembl_transcript_id entrezgene_id    mgi_symbol
1  ENSMUSG00000022543    ENSMUST00000090457         74684 4930451G09Rik
2  ENSMUSG00000079083    ENSMUST00000110582         77532          Jrkl
3  ENSMUSG00000054115    ENSMUST00000110585         27401          Skp2
4  ENSMUSG00000060227    ENSMUST00000110586        319996         Golm2
5  ENSMUSG00000020744    ENSMUST00000135552         67283      Slc25a19
6  ENSMUSG00000038271    ENSMUST00000135559        320678         Iffo1
7  ENSMUSG00000025512    ENSMUST00000166082         68038         Chid1
8  ENSMUSG00000034755    ENSMUST00000192677        245578       Pcdh11x
9  ENSMUSG00000058966    ENSMUST00000207020         68952        Tlcd3b
10 ENSMUSG00000109498    ENSMUST00000207029            NA       Gm45222

Thank you very much.

[Kevin Blighe]

Great - thank you for returning with the extra information