miRNA names from ensemble IDs
2
1
Entering edit mode
7.4 years ago
geneart$$ ▴ 50

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 • 5.9k views
ADD COMMENT
0
Entering edit mode

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 REPLY
3
Entering edit mode
7.4 years ago
Prakki Rama ★ 2.5k

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 COMMENT
1
Entering edit mode

Thanks very much, it worked !

ADD REPLY

Login before adding your answer.

Traffic: 1294 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6