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 , 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)  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) .
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.
 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
 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
 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
 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
 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
 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
This database is hosted and maintained by
Please contact firstname.lastname@example.org for support or inqueries.
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.
The identifiers are based on Ensembl ID version 92
Homology mapping was done with EggNog database. It will be revised soon.
The userbase, use cases and R/Shiny specific properties prefer precompiled tables with optional analytic or display features.
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.