I am trying to compare old microRNA microarray data (aligned to mirBase 17) to NGS sequencing data (aligned to mirBase 19). Because the old data labels some microRNAs as * (star) and mirBase 19 no longer has * sequences, how do I determine whether an old * sequence is now -3p or -5p? I do not want to assume that the lesser expressed -3p or -5p sequence is the star sequence, since I am hypothesizing that exosome microRNAs which may contain higher levels of star sequences than the cells they are derived from.
I found a web tool (http://mirsystem.cgm.ntu.edu.tw/) which makes miRNA name conversion among several versions of miRBase. It may work for you although you could also download previous versions of miRBase and check the names as Ashwani Jha suggested.
Hope this helps.
Unfortunately previous miRBase releases are not available at all. So I guess it would not be possible for you to solve your problem. But one thing we can do is to request the miRBase maintenance and release team to include atleast upto five previous releases. Because before we complete our whole analysis on the current release the next release would be announced. Even I am facing the same problem and I need to work on the miRBase 19 again.
You could individually check the microRNAs by number on the recent miRbase release. For each microRNA it lists the previous IDs. This should answer your question, but it might be slow if you have lots of miRs to check!
Go to miRBase previous releases URL ftp://mirbase.org/pub/mirbase/
download mature mIRNA sequences for all species, write a code in any language you are comfortable to match the sequences of this release (19) with older release. This will sort out your problem. But remember there are many dead miRNAs, whose list is also given at ftp site of miRBase.
You could try annotating the sequences by searching the Applied Biosystems Taqman miRNA assays as the assay is usually named the updated name but the annotation still retains information as to whether its alias was a previous miRNA *(star).
Also, I notice that you are looking at exosome miRNA's. I have recently had a paper accepted to NAR, should be released as advance publication in the next few days, that performed NGS on exosomes miRNA. I did NOT find that exosomes contained a higher level of star sequences although I was unable to do NGS on the cells for comparison due to costs at the time.
I found a web tool (http://mirsystem.cgm.ntu.edu.tw/) which makes miRNA name conversion among several versions of miRBase. It may work for you although you could also download previous versions of miRBase and check the names as Ashwani Jha suggested.
Hope this helps.
If you are interested in extracellular/circulating miRNAs my group has recently developed a database (http://atlas.dmi.unict.it/mirandola/index.html) submitted for publication and it contains a tool (http://atlas.dmi.unict.it/mirandola/tools.php) to convert miRNA IDs (to date the last miRBase version in our tool is 18). For each miRNA ID you can see the available information in our database.
Of course! There is some problem with ResearchGate when you click on the link that i have provided. You should copy and paste the link or you can search it on google! (you can search these keywords on google miRandola microRNA database too)
Dear Russo,
I looked your provided tool that is very interesting But this is only for Human, it is not possible to integrate it for other organism ??? for instance Zebra fish ??
Thanks in advance and waiting for your input
I am agree with Ashwani, and you just check the release note of MIRBASE
The question is old, but I solve this using the aliases file provided by mirbase. A suitable R script is also attached.
ftp://mirbase.org/pub/mirbase/CURRENT/aliases.txt.zip
https://gist.github.com/mlist/7c0fd892e137d3810917
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