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miRNA names from ensemble IDs

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
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updated by Ram Ram • written by geneart$$ • geneart$$

2 answers

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
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updated by Ram Ram • written by Prakki Rama Prakki Rama

Well what I meant by miRBASE name is like bta-mir-26a-2 and so on. It is the miRBASE ID . so I f I input my enseble IDs like ENSBTAG00000029979 then I need to see how I can get a miRBASE ID for it, using miRBASE database.Thanks :)

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updated by Ram Ram • written by geneart$$ • geneart$$

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