I have a list of miRNAs and a list of predicted target mRNAs. The mRNA targets were created by other ways.
I am searching for a tool to test whether an interaction (binding) could exist between both list. I want to use both lists as inputs in this tool.
Any suggestions ?
Hi Mohamed Samir ,
I've recently made an R pipeline for this purpose (attached as a pdf). In essence, I used the "multiMir" R package to identify putative and empirical interactions between a list of microRNA (based on microRNA-sequencing) and mRNA (via RNA-sequencing data). This approach compiles 8 predictive algorithms and validated interaction databases into the analysis: predicted (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and validated (miRecords, miRTarBase and TarBase).
I actually need a simple tool to visualize the interaction of miRNA and mRNA and to show a network of this.
I have both lists.
Hi Mohamed, do you have an “adjacency matrix” of the interactions yet, or are you still looking to identify the putative interactions before visualizing them? If you still need to develop the interactions-based “adjacency” matrix, you can use Targetscan to identify them. Alternatively, just message me your lists and I’ll do it (should only take 5 minutes to do).
Hey Mohamed. please try miRGate. With this you can analyze miRNA and gene isoforms lists.
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