Welcome to RBP2GO


RBP2GO is a comprehensive database dedicated to the analysis of RNA-binding proteins, their interactions and functions. RBP2GO offers three search options for each species, which can be accessed via the sidebar under SEARCH SPECIES. More details can be found in the HELP menu.



Species

13

RBP candidates

22552







References

RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2020.

R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Caudron-Herger et al. Molecular Cell 2019.

Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Caudron-Herger et al. Nature Protocols 2020.


A database on RNA-dependent proteins (R-DeeP) is also available here.





RBP candidates

6100

Homo sapiens

Human Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
Limited to CGC Genes
GO List






RBP candidates

2897

Mus musculus

Mouse Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

311

Danio rerio

Zebrafish Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

2982

Drosophila melanogaster

Fly Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

1873

Caenorhabditis elegans

C. elegans Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

2155

Saccharomyces cerevisiae

S. cerevisiae Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

2352

Arabidopsis thaliana

A. thaliana Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

169

Trypanosoma brucei

T. brucei Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

79

Leishmania donovani

L. donovani Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

1162

Leishmania mexicana

L. mexicana Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

1030

Plasmodium falciparum

P. falciparum Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

226

Salmonella enterica subsp. enterica ser. Typhimurium

S. enterica Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






RBP candidates

1216

Escherichia coli

E. coli Protein of Interest

Enter a protein ID, gene name or protein name into the search field:

Search Result



Gene Ontology

Enter a Gene Ontology (GO) term or a keyword into the search field:

Search Result


Advanced search option including search for list of proteins or GO terms.

Protein List
GO List






Data Download


  • In this section, all datasets used in the RBP2GO database are available for download.

  • IMPORTANTLY, the datasets contain a large amount of information, in particular, the complete GO trees are included, so that the datasets are not displayed properly e.g. in Excel. Therefore, we recommend to work with these datasets using for example RStudio or other suitable programs of your choice.

  • The dataset sizes range from about 400 KB to 105 MB.




Homo sapiens


Mus musculus


Danio rerio


Drosophila melanogaster


Caenorhabditis elegans


Saccharomyces cerevisiae


Arabidopsis thaliana


Trypanosoma brucei


Leishmania donovani


Leishmania mexicana


Plasmodium falciparum


Salmonella Typhimurium


Escherichia coli




All species





References and Links

Reference Table

R-DeeP and RBP Studies


Species Specific Databases


Proteins and Protein-Protein Interactions Databases


Intrinsically Disordered Proteins and Low Complexity Domains


Coiled-coil Prediction


Gene Ontology


Diseases


Isoelectric point


Databases Collections


Literature Search


Icons and Webpage





Help and Documentation


  • RBP2GO is a comprehensive database dedicated to the analysis of RNA-binding proteins, their interactions and functions. RBP2GO offers three search options for each species, which can be accessed via the sidebar under SEARCH SPECIES.

  • The Protein Search and the GO Search options can be used to search the database for single proteins and GO terms respectively. The button About the Format gives more details about the possible input formats.

  • The Advanced Search offers the possibility to search simultaneously for a list of proteins and/or a list of GO terms. In addition, a range of isoelectric points (pI) can be selected when available. For Homo sapiens the search can even be limited to the CGC genes.

  • The RBP2GO score reflects the likelihood of a protein binding to RNA on a scale from 0 to 100 and is derived from the total number of listings of this protein in proteome-wide RBP/R-DeeP studies of the respective species as well as the average number of listings of its top ten interaction partners according to the String interaction score. Next to the RBP2GO score, the listing score of the proteins (number of times the each protein is listed as RBP) is indicated as well as the average listing score of the top ten interactors according to the STRING database.

  • The search results can be downloaded depending on the content as CSV or TXT files for further processing.

  • The full reference table is available for download under the menu REFERENCES.

  • The sidebar is dynamic and can be removed by clicking on the list icon next to the RBP2GO logo at the top left corner of the screen.



A detailed and user-friendly documentation can be downloaded here:



A short tutorial video is also available:




About RBP2GO

How to cite

Manuscript accepted: 16 November 2020

RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2020.



Related publications

R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Caudron-Herger et al. Molecular Cell 2019.

Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Caudron-Herger et al. Nature Protocols 2020.



Related database



Contact

The authors of the RBP2GO database can be contacted at the following email address

databases.diederichslab(at)dkfz.de