List of Ensembl Transcript IDs corresponding to protein-coding genes

Question

[Kristin Muench]

Hello,

Does anyone know where I can find a list of Ensembl transcript IDs (e.g., ENST0000011111) associated with protein-coding genes?

I've run my mRNA-Seq data through kallisto and am plotting PCA on the pseudocounts, which are associated with Ensembl Transcript IDs. A labmate wonders if my PCA would cluster better if I only used the rows of counts corresponding to Ensembl Transcript IDs associated with mRNA (since, presumably, all of the other rows would be 0, since the sequencing was only done on mRNA, not ncRNA).

I'm not sure to what extent removing rows of 0s would change my PCA, but I thought I'd give it a try.

Thanks for your help!

Answer 1

[mehran.karimzade]

Go to:

http://www.ensembl.org/biomart/martview/21893b6a5bf91112c9a786f296b9200d

Choose database > Ensembl Gene 83 > Homo sapiens

Attributes > Gene > click on Ensembl Protein ID (or any other protein IDs such as refseq, etc.)

go to results and download

Answer 2

[EagleEye]

Use GTF from ensembl

ftp://ftp.ensembl.org/pub/release-83/gtf/homo_sapiens