I am struggling with the IDs of circRNA microarray from Arraystar and their correspondences with general circRNA databases such as circBase.
Some of you have used this service from Arraystar?. Do you have access to the conversion rules between Arraystar circRNA probes and the circBase IDs?. It looks that many people published results using the Arraystar IDs.
Thanks in advance.
Dear Noor
Thank for the advice... however still I miss a correspondence between ALL the Arraystar circRNA names and circBase. Do you have this info?
Best
Thanks for the question...I was also wondering. For human, anyway, Arraystar seems to use a five-digit designation that doesn't have any obvious connection to the circBase IDs. It does appear, however, that Arraystar includes the circBase IDs on the report it sends to the customer. Haven't tried it myself, though.
Kenneth
The problem that you pointed out it is clear. Several papers in good journals such as this one in Eur Heart J (https://www.ncbi.nlm.nih.gov/pubmed/26802132) are describing cirRNA using the nomenclature of Arraystar without making a link to the "official" symbols and even with no reference to the genomic coordinates of the circRNA, or the exons involved. I have contacted those authors but unfortunately I got no answer from them. Not good.
On the other hand, Arraystar does not provide the nomenclature conversion to the general public, only, as you said, when you request their services.
You may already know this, but in GEO, two platforms have been deposited, for V1 and V2:
V1: GPL19978
V2: GPL21825
The columns include "ID" and "circRNA", but I don't think either of these corresponds to circBase. However, the probe sequence is included as the final column, so this might permit a cross-check.
Hi Hawking
Still not.. I wrote an email, but no answer. Still waiting.
Hope you have best luck
For GPL19978 download this Data S2 Table
and check annotation columns it helped me
Can anyone help with this conversion from arraystar to circbase for mus. Dr. Satarupa Banerjee provided the human resources.
For the conversion of the circular rna IDs, you can use the following tool, for which link is given below :
http://159.226.67.237:8080/new/Liftover.php
I completely agree with Francesco. Arraystar claims to identify circRNAs but is not competent enough. Further, its chip has limited circRNAs as compared to deep RNA sequencing.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA