Welcome to R-DeeP 3.0


R-DeeP 3.0 is a database on RNA-dependent proteins in unsynchronized HeLa S3 and A549 cells, and during either mitosis or interphase synchronized HeLa S3 cells resulting from the concept of RNA dependence and its experimental conversion


Advanced Search

Single Search

Search for RNA-dependent proteins in all R-DeeP 3.0 cell lines and enter lists of proteins to your search.



Search for RNA-dependent proteins in a specific cell line
Proteins of Unsynchronized Cells
Proteins of Synchronized Cells
Related References
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.
RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2021.
Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells. Rajagopal et al. Cancers 2022.
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins. Wassmer et al. Nucleic Acids Research 2024.





R-DeeP proteins

4765

HeLa S3 cells

Human Protein of Interest

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

Search Result





R-DeeP proteins

3743

A549 cells

Human Protein of Interest

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

Search Result





R-DeeP proteins

7069

HeLa S3 synchronized cells - Interphase

Human Protein of Interest

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

Search Result





R-DeeP proteins

7152

HeLa S3 synchronized cells - Mitosis

Human Protein of Interest

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

Search Result





Help and Documentation


  • R-DeeP 3.0 is a database on RNA-dependent proteins in HeLa S3 and A549 cells, as well as HeLa S3 synchronized in mitosis and interphase, resulting from the concept of RNA Dependence and its experimental conversion. R-DeeP 3.0 offers several search options, which can be accessed via the sidebar.

  • The Advanced search offers the possibility to search simultaneously for a list of proteins in all datasets simultaneously. The result of the search indicates already for each protein whether data is available or not, and whether the protein is presenting an RNA-dependent shift or not.

  • The Single search option can be used to search the database for single proteins in each of the dataset respectively. The button About the Format gives more details about the available input formats that can be used to search for a protein of interest.

  • The search results can be downloaded depending on the content as CSV, PDF or HMTL files for archiving or further data processing and analysis.

  • The References menu offers a selection of helpful links to proteins-related databases, protein-protein interactions databases, and RNA-binding-related databases and publications

  • Information on how to cite and related publications and databases can be found under the About section from the sidebar menu.

  • The sidebar is dynamic and can be removed by clicking on the list icon next to the R-Deep 3.0 logo at the top left corner of the screen.



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

User Guide

A detailed analysis pipeline and test dataset including examples can be downloaded here:

Analysis Pipeline





References and Links

Proteins and Protein-Protein Interactions Databases

UniProt

Ensembl

Human Protein Atlas

KEGG PATHWAY Database

STRING database

CORUM database

InterPro

Pfam


Gene Ontology

Gene Ontology Consortium

QuickGO


R-DeeP and RBP Studies

Ashburner et al. 2000

Bach-Pages et al. 2020

Backlund et al. 2020

Baltz et al. 2012

Bao et al.2018

Beckmann et al. 2015

Boucas et al. 2015

Brannan et al. 2016

Bunnik et al. 2016

Castello et al. 2012

Castello et al. 2016

Caudron-Herger et al. 2019

Conrad et al. 2016

Cook et al. 2011

De Pablos et al. 2019

Despic et al. 2017

Du et al. 2020

Esmaillie et al. 2019

Garcia-Moreno et al. 2019

Gerstberger et al. 2014

He et al. 2016

Hendrickson et al. 2016

Huang et al. 2018

Ignarski et al. 2019

Kramer et al. 2014

Kwon et al. 2013

Liao et al. 2016

Liepelt et al. 2016

Lueong et al. 2016

Mallam et al. 2019

Marondedze et al. 2016

Matia-González et al. 2015

Milek et al. 2017

Mitchell et al. 2013

Mullari et al. 2017

Nandan et al. 2017

Panhale et al. 2019

Perez-Perri et al. 2018

Queiroz et al. 2019

Ray et al. 2013

Reddy et al. 2015

Reichel et al. 2016

Scherrer et al. 2010

Shchepachev et al. 2019

Sundararaman et al. 2016

Sysoev et al. 2016

The Genome Ontology Consortium et al. 2019

Treiber et al. 2017

Trendel et al. 2019

Ashburner et al. 2000

Tsvetanova et al. 2010

Urdaneta et al. 2019

Wessels et al. 2016

Zhang et al. 2016


Diseases

Cancer Gene Census

Cosmic database

TCGA

OMIM

ClinGen


Icons and Webpage

EBI icons

Font Awesome

Gallery - R-Shiny - RStudio


About R-DeeP 3.0

How to cite

Published: March 2025
Rajagopal, V. et al. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. Nat. Commun. 16, 2325 (2025).

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.
RBP2GO: A comprehensive, pan-species database on RNA-binding proteins, their interactions and functions. Caudron-Herger et al. Nucleic Acids Research 2021.
Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells. Rajagopal et al. Cancers 2022.
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins. Wassmer et al. Nucleic Acids Research 2024.

Related databases

R-DeeP: Database for RNA-dependent Proteins

RBP2GO: A Comprehensive Database of RNA-Binding Proteins and their Functions


Contact

The authors of the R-DeeP 3.0 database can be contacted at the following email address

database.rdeep(at)dkfz.de


     © 2024 - ( RNA-Protein Complexes & Cell Proliferation - DKFZ Heidelberg )
Rajagopal et al. Nature Communications, 2025