How to view if a gene is protein-coding?

Question

[DN99]

I have a list of genes, I'm not experience with bioinformatics tools so I'm look to see if all of these genes are protein coding or if they are of any other gene types - is there a tool where I am input a gene list to check this? My gene list is 200 genes of HGNC gene symbols.

Answer 1

[Sam]

You can check out Ensembl's BioMart. Choose Ensembl genes, select Human, then add Gene Type in Attributes and key in your gene names in the filter under Input external references ID list

Answer 2

[fracarb8]

You can use biomaRt, and the gene_biotype attribute.

library("biomaRt")
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
myResult <- getBM(values = yourListofGenes, attributes = c("ensembl_gene_id", "gene_biotype"), mart=mart)

I am a bit rusty with biomaRt, but the syntax should be crrect.

[swbarnes2]

Note that genes have many transcripts, and while each transcript should have exactly one biotype, different transcripts for the same gene might very well have different biotypes.

[fracarb8]

biomaRt can give you all the transcripts. You need to play with the attributes values, and add the transcripts (ensemble_transcript_id not sure of the spelling). Have a look the listAttributes() and all the ?getBM options.