Question: circRNA - miRNA ceRNA network construction
gravatar for Barry Digby
9 months ago by
Barry Digby630
National University of Ireland, Galway
Barry Digby630 wrote:

Hi all,

I wanted to discuss how circRNA - miRNA interactions are predicted, I'm hoping some of you could shed some light on this for me. The common method in literature to achieve this can be summarised as follows:


The CSCD and circinteractome web servers are great, but I want to know how I can automate this process for hundreds of DE circRNAs. Unfortunately circinteractome download files do not have the corresponding miRNA predictions for circRNAs. CSCD offer MRE files, where genomic locations of each MRE and their corresponding miRNA are available.

Is the best strategy to use the genomic coordinates of a circRNA and extract all MRE + miRNAs from the CSCD MRE file? Or am I going about this the wrong way? Papers do not seem to offer any more information that is available above. Any pointers would be greatly appreciated.



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