Select a miRNA collection


Extra collection information


                      
                    

                    

                      

                        
                        

                          
                          
                        

                      

                      

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        

                        

                          Type in the first 
                          few letters of a gene name to populate the list
                        

                        
                        

                        

                          
                          

                            
                            
                          

                        

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        
                      

                    

                  

                

              

            

          

          

            

              

                

                  

                    

                      
                      

                        
                        
                      

                    

                  

                  

                    
                    

                    
                    

                    
                  

                  

                    The conservation status of miRNAs is obtained from
                    TargetScan
                  

                  

                    

                      

                        
                      

                    

                  

                  

                    
                  

                

              

            

          

          

            

              

                

                  

                    
                    
                  

                  

                    
                    
                  

                  

                    
                    
                  

                

              

            

            

              

                

                  

                    

                      
                    

                  

                  

                    

                      
                    

                  

                

              

            

          

          

            

              

                

                  

                   
                

              

              

                

                  

                

              

            

            

              

                

                  

                    
Display sites along transcript

                    

                      
                    

                  

                  

                    
                    

                      Hover on points to view details, and click to 
                      visualize the alignment on the target sequence. You may
                      also select miRNAs to show/hide by clicking on the legend.
                    

                    
                    

                      

                        
                        
                      

                    

                    

                      

                        

                          
                        

                      

                    

                  

                

              

              

                

                  

                    
Aggregated per miRNA

                    

                      
                    

                  

                  

                    
                    

                      

                        Download all
                      

                    

                    

                      
                    

                  

                

              

              

                

                  

                    
Table

                    

                      
                    

                  

                  

                    

                      

                        

                          Double click on a row to visualize the alignment
                           on the target sequence.
                        

                      

                      

                        
                        
                      

                    

                    
                    

                      Download all
                    

                  

                

              

            

            

              

                

                  
Cached hits

                  

                    
                  

                

                

                  

                  

                  
                  
                

              

            

          

          

            

              

                

                  

                    
                    

                      
                      
                    

                  

                

              

              

                TargetScan conservation status
                

              

              

                
              

            

            

              

                

                  

                    
Affinity plot

                    

                      
                    

                  

                  

                    
                  

                

              

            

            

              

                

                  

                    
Targets

                    

                      
                    

                  

                  

                    

                  

                

              

            

          

          

            

              

                

                  
miRNA binding prediction

                

                

                  

                    
                    

                      micro-RNAs (miRNAs) regulate transcripts stability and 
          translation by targeting the Argonaute complex to RNAs exhibiting a 
          partial complementarity with, in particular, the miRNA's seed 
          sequence. For a general review on miRNA biology and targeting, see
               Bartel (2018).
                      McGeary, Lin et al. (2019)
                       have additionally shown the 
      relevance of flanking nucleotides by empirically measuring the affinity 
      (specifically the dissociation rate constant, KD) of a set of miRNAs to 
      random 12-mer sequences, and then computationally extrapolating to other 
      miRNAs). The scanMiR package, to which this app is an 
      interface, builds on this work to offer a powerful and flexible binding 
      and repression prediction framework.
                    

                  

                

              

            

            

              

                

                  
Getting started

                

                

                  

                    

                      For a quick tour of the app, click here.
                    

                    
There are two main ways to use scanMiRApp:

                    

                    
Transcript-centered:

                    

                      In the 'Search in gene/sequence' menu, you'll be able to 
                      scan the sequence of a given transcript for binding sites 
                      of (sets of) miRNA(s).
                    

                    

                    
miRNA-centered:

                    

                      In the 'miRNA-based' tab on the left, you'll be able to 
                      visualize information relative to a selected miRNA, 
                      including for instance its general binding profile and its
                      top targets.
                    

                  

                

              

            

            

              

                The shiny app was developed by Pierre-Luc Germain and 
                Michael Soutschek in the context of broader research in the Schratt lab.
                

                Bugs reports and feature requests are welcome on the github repository.