Question: miRNA names from ensemble IDs
1
gravatar for geneart$$
6.5 years ago by
geneart$$40
United States
geneart$$40 wrote:

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 :)

rna-seq • 5.0k views
ADD COMMENTlink modified 6.5 years ago by Prakki Rama2.4k • written 6.5 years ago by geneart$$40

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

ADD REPLYlink written 6.5 years ago by Neilfws49k
2
gravatar for Prakki Rama
6.5 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

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
ADD COMMENTlink modified 10 months ago by RamRS30k • written 6.5 years ago by Prakki Rama2.4k

Thanks very much, it worked !

ADD REPLYlink written 6.5 years ago by geneart$$40
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