miRNA names from ensemble IDs

Question

[geneart$$]

Hi I am learning to perform RNA seq analysis, specifically miRNA expression analysis using DESeq2. I have a list of miRNA differentially expressed between my control and treated samples. I have their ensembl IDs and am looking to get their corresponding miRBASE name like mir-XX-XXX and so on.

miRBASE has no option of using ensembl IDs to get the names out. I looked into ENsembl website and they have a BioMArt option where you can upload your file to get information out. The output I was hoping will be that each of my gene_ID that I have in my file will endup having a miRBASE name but it is not what it looks like.

Anyone has any other options that you might suggest? Greatly appreciate your suggestion ! Thanks :)

[Neilfws]

Can you link to an example of what you think is a mirBASE "name"? I do not see identifiers of the form that you describe; names seem to be in the form e.g. hsa-mir-675.

http://www.mirbase.org/help/nomenclature.shtml

Answer 1

[Prakki Rama]

You could get it by using Biomart.

1. Choose your database first - I selected Ensembl genes 75, Bos tauras genes
2. Click 'Filters' - paste your Ensembl Gene ID's under "Gene", "ID list limit"
3. Then click "Attributes" - Tick the miRBase ID(s)
4. Click Results - You should see the following output

Ensembl Gene ID         Ensembl Transcript ID  miRBase ID(s)
ENSBTAG00000029979      ENSBTAT00000042358     bta-mir-126

[geneart$$]

Thanks very much, it worked !