RBPbase v0.2.1 alpha

A COMPREHENSIVE DATABASE OF EUKARYOTIC RNA-BINDING PROTEINS (RBP) WITH THEIR RBP ANNOTATIONS


Welcome to RBPbase, a database that integrates high-throughput RNA-binding protein (RBP) detection studies. For context, we recommend our review on RNA-binding proteins [1], and the technical descriptions of RNA interactome capture (RIC) [2,3,4], a mass spectrometry (MS) based protocol. The latest refinements of this protocol include enhanced RIC (eRIC) [5] and many others which can be found under tab 'Studies'.


We accelerated the release of this first public version in response to the SARS-CoV-2 crisis. We will continuously introduce refinements and welcome feedback. While no SARS-CoV-2 RNA interactome is currently available, SARS-CoV-2 proteomics are already underway. Since SARS-CoV-2 is an RNA virus, it is expected to intensively use host RBPs for its replicative cycle. We hope that RBPbase will help to identify relevant host proteins as RBPs, which could be helpful for understanding viral biology and ultimately the design of therapeutic strategies. To support SARS-CoV-2 research the database also provides annotations for 332 experimentally validated SARS-CoV-2-human protein-protein interactions (PPIs) [6].


In these early versions, RBPbase functions as a table browser with search, filtering and downloading functions. We are committed adding latest high-throughput RBP interaction studies and annotations. In near future, RBPbase will get more sophisticated analysis and plotting functions to analyse your RIC studies here. Stay tuned.



            

            

            

              

                References:
                

                [1] Hentze, M.W., Castello, A., Schwarzl, T. and Preiss, T., 2018. A brave new world of RNA-binding proteins. Nature Reviews Molecular Cell Biology, 19(5), p.327.
                https://doi.org/10.1038/nrm.2017.130
                

                [2] Baltz, A.G., Munschauer, M., Schwanhäusser, B., Vasile, A., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M. and Wyler, E., 2012. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell, 46(5), pp.674-690.
                https://doi.org/10.1016/j.molcel.2012.05.021
                

                [3] Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M. and Krijgsveld, J., 2012. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149(6), pp.1393-1406.
                https://doi.org/10.1016/j.cell.2012.04.031
                

                [4] Castello, A., Horos, R., Strein, C., Fischer, B., Eichelbaum, K., Steinmetz, L.M., Krijgsveld, J. and Hentze, M.W., 2013. System-wide identification of RNA-binding proteins by interactome capture. Nature protocols, 8(3), p.491.
                https://doi.org/10.1038/nprot.2013.020
                

                [5] Perez-Perri, J.I., Rogell, B., Schwarzl, T., Stein, F., Zhou, Y., Rettel, M., Brosig, A. and Hentze, M.W., 2018. Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nature communications, 9(1), pp.1-13.
                https://doi.org/10.1038/s41467-018-06557-8
                

                [6] Gordon, D.E., Jang, G.M., Bouhaddou, M., Xu, J., Obernier, K., O'meara, M.J., Guo, J.Z., Swaney, D.L., Tummino, T.A., Huttenhain, R. and Kaake, R.M., 2020. A SARS-CoV-2-human protein-protein interaction map reveals drug targets and potential drug-repurposing. BioRxiv.
                https://doi.org/10.1101/2020.03.22.002386
              

            

          

        

      

      

        

          

            

              

                

                  

                    

                      

                        

                          
                          

                            
                            
                          

                        

                      

                    

                    

                      
                    

                    

                      
                    

                    

                      

                    

                  

                

              

            

          

          

            

              

            

          

        

      

      

        

      

      

        

          

            

              

            

          

        

      

      

        

          

            

              
About

              
Impressum

            

            

              
                
              
              

              

                This database is hosted and maintained by
                

                

                  Hentze Group
                  

                  European Molecular Biology Laboratory (EMBL)
                  

                  Thomas Schwarzl, PhD, Staff Scientist in Hentze and Huber Group
                  

                  Meyerhofstraße 1
                  

                  69117 Heidelberg.
                

              

              

                Please contact
                biohentze@embl.de
                for
                  support or inqueries.
              

            

            

              
FAQ

              
Frequently asked questions

              

            

            

              
Is the input data, code or shiny app available?

              All code for the backend data generation can be
                           found in this git repository:
              https://git.embl.de/schwarzl/rbpbasebackend
              . The shiny app and Dockerfile can be
                           found in this git repository: 
              https://git.embl.de/grp-hentze/rbpbase
            

            

              
Why summarizing by gene identifiers
                            and not protein identifiers?

              
The common identifiers were individually selected
                    for each organism. Because protein identifiers are very
                    unstable, gene identifiers were used to summarize
                    reported RBPs. If any isoform of a protein was reported,
                    the gene was marked as RNA-binding.
                    To account for different genomic locations,
                    unique identifiers were created from the reported
                    gene names. If any of the gene identifiers was reported
                    to be RNA-binding, the unique identifier was marked
                    as RNA-binding. Genes without gene names kept their
                    genomic identifier.

            

            

              
What Ensembl versions are the identified based on?

              
The identifiers are based on Ensembl ID version 92

            

            

              
How was the homology mapping done?

              
Homology mapping was done with EggNog database[1].
                    It will be revised soon.

            

            

              
Why is RBPbase a table browser and not a relational database?

              
The userbase, use cases and R/Shiny specific properties prefer
                           precompiled tables with optional analytic or display features.

            

            

              [1] Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P., 2007. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic acids research, 36(suppl_1), pp.D250-D254.
              https://doi.org/10.1093/nar/gkm796
            

            

              
Acknowledgements

              
Thank you very much

              

            

            

              
Eva Schitter for the work on homology mapping during an intership at the Hentze lab.

              

              
Wolfgang Huber for advice and feedback.

              

              
Josep Manel Andres Moscardo and EMBL IT Services for hosting the Shiny App and EMBL Bio-IT for hosting Gitlab services.