How to filter out the non-coding genes?

Question

[liux.bio]

Hi,

Biostars. I have a list of genes with Ensembl gene ids and I want to filter out non-coding genes and get protein-coding genes. I am using Bioconductor package BiomaRt, but can't find a direct way. Any suggestions?

Many thanks!

[Scott McKay]

Can you use the R script you used to figure this out? I am trying to do something similar now and am having trouble.

Answer 1

[Prakki Rama]

I used Transcript Biotype in the attribute to check if it is actually protein coding or not. It seems pretty straightforward using Biomart.

[liux.bio]

Got it. Thank you!

Answer 2

[Scott McKay]

Can you post the R script you used to figure this out? I am having a terribly hard time trying to do something similar here.

[piyushjo]

Use the biomaRt vignette. If you have ids as ensembl gene ids it is pretty easy. Let x be a character array with your ensembl gene ids (with and without version information)

goids = getBM(attributes = c('ensembl_gene_id', 'gene_biotype'), 
              filters = 'ensembl_gene_id', 
              values = x, 
              mart = ensembl)

Below is the information for gene biotypes.

https://useast.ensembl.org/info/genome/genebuild/biotypes.html

Also I think you should add your post as comment rather than answer.