Converting lincRNA Ensembl id to gene symbol

Question

[ek699]

Hi, I am trying to convert Ensembl id of lincRNA to its symbol (gene name) by using biomaRt in R, but the dataset doesn't give me a proper annotation. I know that Ensembl has the annotation for this lincRNA, since I can see it on IGV. For your information, I used GRCh38. p13 annotation from GENCODE when I mapped the reads.

I simplified my code as much as possible just to see if the biomaRt provides me a proper annotation for the lincRNA gene, but it gives me NA.

library(biomaRt)
fix_name <- as.character("lincRNA_id")
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
symbol <- getBM(filters = "ensembl_gene_id",
                attributes = c("ensembl_gene_id","hgnc_symbol"),
                values = fix_name, 
                mart = mart)

 >symbol
  ensembl_gene_id hgnc_symbol
1 lincRNA_id          NA

Could you please let me know how I can get the gene name from the id? I am new to bioinformatics, so any help is much appreciated. Thank you

Answer 1

[ATpoint]

It is not uncommon that some genes do not have a HGNC symbol, especially non-coding genes.

symbol <- getBM(attributes = c("ensembl_gene_id","hgnc_symbol"),
                             mart = useMart("ensembl", dataset="hsapiens_gene_ensembl"))

## Almost 25000 Ensembl genes have no HGNC symbol
sum(symbol$ensembl_gene_id != "") ## 67159
sum(symbol$hgnc_symbol != "") ## 42848

Code for that plot:

library(biomaRt)
library(ggplot2)

symbol <- getBM(attributes = c("ensembl_gene_id","hgnc_symbol", "gene_biotype"),
                mart = useMart("ensembl", dataset="hsapiens_gene_ensembl"))

## Almost 25000 Ensembl genes have no HGNC symbol
sum(symbol$ensembl_gene_id != "") ## 67159
sum(symbol$hgnc_symbol != "") ## 42848

df <- data.frame(table(symbol[symbol$ensembl_gene_id != "" & 
                              symbol$hgnc_symbol == "",]$gene_biotype)) %>% arrange(Freq)
colnames(df) <- c("Gene_Biotype", "Number")

df$Gene_Biotype <- factor(df$Gene_Biotype, levels = df$Gene_Biotype)

ggplot(data=df, aes(x=Gene_Biotype, y=Number)) +
  geom_bar(stat="identity") + 
  coord_flip() + 
  ggtitle("Genes without HGNC symbol")

[ek699]

Thanks for your comment. Is there any way that I can get gene name from this lincRNA gene id?

[ATpoint]

Did you read my answer? If your gene has no HGNC symbol, then no, you can't get HGNC name for it.