How to find transposable element genes in ensembl annotation

Question

[james.lloyd]

I have some differential genes from an RNA-seq experiment and I wanted to look at changes of transposable element genes (transposons). This data is human and I have the ensembl gene names from GRCh37 and the GRCh37.75 GTF. I wanted to add the gene_biotype from the GTF to each gene and look for different types of genes, protein coding vs miRNA and transposable element etc. But now I have look at the biotypes, I see that transposable element are not in the list. I do not know what they fall under. Is there any way to annotate my ensembl genes that are transposable elements as such?

I thought that this would work because I did this for Arabidopsis using TAIR10 and the gene_type separated all of these features out but biotypes do not pair well with the annotations used by TAIR. Any help would be appreciated!

Answer 1

[Michael]

I think they are not annotated in the biotype as a class of its own. Did you try searching ensembl.org for transposon? Transposons are repeats identified by RepeatMasker. To display Transposons in the Ensembl genome browser, open a genome region and click Configure this page, then scroll down to and click Repeat regions on the left, activate those repeat regions that interest you. Use Export data to get the data you need in GTF or any other supported format.

The result could be like this:

http://www.ensembl.org/Homo_sapiens/Share/641b6b78335fb4da76e87f6a6496dfab205851174

Answer 2

[abascalfederico]

Using bedtools to determine whether the (RNAseq) expressed exons overlap annotated repeat elements may be of help. All you need is to have the coordinates of both; you can retrieve RepeatMasker annotations from UCSC easily.

HTH,