Question: List of Ensembl Transcript IDs corresponding to protein-coding genes
gravatar for Kristin Muench
4.7 years ago by
United States
Kristin Muench520 wrote:


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!

rna-seq pca ensembl • 3.6k views
ADD COMMENTlink modified 4.7 years ago by EagleEye6.7k • written 4.7 years ago by Kristin Muench520
gravatar for mehran.karimzade
4.7 years ago by
mehran.karimzade180 wrote:

Go to:

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

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by mehran.karimzade180
gravatar for EagleEye
4.7 years ago by
EagleEye6.7k wrote:

Use GTF from ensembl

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by EagleEye6.7k
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