Looking up Gene IDs in R

Question

[cthangav]

Hello, Given a list of gene names, I need to create a table containing the Ensemble ID, chromosome, start, end of that gene. Example:

##             ens_id        gene            view  chr start   end
## 1: ENSG00000243485 MIR1302-2HG Gene Expression chr1 29553 30267
## 2: ENSG00000237613     FAM138A Gene Expression chr1 36080 36081
## 3: ENSG00000186092       OR4F5 Gene Expression chr1 65418 69055

What command can I use to look up ensemble IDs and start/end locations of genes?

Answer 1

[rpolicastro]

The biomaRt library is great for this.

library("biomaRt")

genes <- c("MIR1302-2HG", "FAM138A", "OR4F5")

ensembl <- useEnsembl("genes", "hsapiens_gene_ensembl")

gene_info <- getBM(
  mart=ensembl,
  attributes=c("ensembl_gene_id", "external_gene_name", "gene_biotype",
    "chromosome_name", "start_position", "end_position", "strand"),
  filters=list(external_gene_name=genes))

> gene_info
  ensembl_gene_id external_gene_name   gene_biotype chromosome_name
1 ENSG00000243485        MIR1302-2HG         lncRNA               1
2 ENSG00000237613            FAM138A         lncRNA               1
3 ENSG00000186092              OR4F5 protein_coding               1
  start_position end_position strand
1          29554        31109      1
2          34554        36081     -1
3          65419        71585      1

See the documentation for more information.

[cthangav]

Thank you, I was able to get this to work for a short list of genes. For my full list of genes, I get this error

Error in getBM(mart = ensembl, attributes = c("ensembl_gene_id", "external_gene_name",  : 
  object 'genes' not found

My guess is because some of the gene names might not be correct "external gene name". Is there a way to filter out those genes, or at least do a quality control check to see if a given gene name is recognized by ensemble?

[rpolicastro]

Can you post the full command you're running?

[cthangav]

Here is the code I am using- I am able to do it with the first few genes in my list:

> library("biomaRt")
> genes <- c("0610005C13Rik", "0610007P14Rik", "0610009B22Rik", "0610009L18Rik", "0610009O20Rik", "0610010B08Rik", "0610010F05Rik", "0610010K14Rik", "0610011F06Rik", "0610012G03Rik", "0610030E20Rik", "0610031O16Rik")
> ensembl <- useEnsembl("genes", "mmusculus_gene_ensembl")
> gene_info <- getBM(
+   mart=ensembl,
+   attributes=c("ensembl_gene_id", "external_gene_name", "gene_biotype",
+                "chromosome_name", "start_position", "end_position", "strand"),
+   filters=list(external_gene_name=genes))
> gene_info
     ensembl_gene_id external_gene_name   gene_biotype chromosome_name start_position end_position strand
1 ENSMUSG00000042208      0610010F05Rik protein_coding              11       23514961     23583639     -1
2 ENSMUSG00000107002      0610012G03Rik protein_coding              16       31765868     31767312     -1
3 ENSMUSG00000099146      0610031O16Rik         lncRNA               3      137916477    137946166     -1
4 ENSMUSG00000043644      0610009L18Rik         lncRNA              11      120239504    120242016      1
5 ENSMUSG00000007777      0610009B22Rik protein_coding              11       51576213     51579701     -1
6 ENSMUSG00000109644      0610005C13Rik         lncRNA               7       45217218     45224751     -1
7 ENSMUSG00000058706      0610030E20Rik protein_coding               6       72324300     72330131      1
8 ENSMUSG00000020831      0610010K14Rik protein_coding              11       70126032     70128740     -1

But when I paste all my genes I get errors. It might be a syntax error somewhere.

 genes <- c("0610005C13Rik", "0610007P14Rik", "0610009B22Rik", "0610009L18Rik", "0610009O20Rik", "0610010B08Rik", "0610010F05Rik", "0610010K14Rik",...
+ gene_info <- getBM(
+   mart=ensembl,
+   attributes=c("ensembl_gene_id", "external_gene_name", "gene_biotype",
Error: unexpected symbol in:
"  mart=ensembl,
  attributes=c("ensembl_gene_id"
                "chromosome_name", "start_position", "end_position", "strand"),
Error: unexpected ',' in "               "chromosome_name","
filters=list(external_gene_name=genes))
Error: unexpected ')' in "  filters=list(external_gene_name=genes))"

I copy/paste the list of genes from a text file (see below)- is there a better way to load my genes into the genes object?

Thank you

[rpolicastro]

If you have all of your genes in a text file load them into R programmatically instead of with copy/paste.

library("stringr")
library("readr")

gene_file <- "genes.txt"

genes <- gene_file %>%
  read_file %>%
  str_extract_all('(?<=\\")[[:alnum:]\\-_.]+(?=\\")', simplify=TRUE) %>%
  as.character

[cthangav]

Thank you, this worked!